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Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for casework. Forensic Science International: Genetics Supplement Series 2022. [DOI: 10.1016/j.fsigss.2022.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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2
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Peng G, Pakstis AJ, Gandotra N, Cowan TM, Zhao H, Kidd KK, Scharfe C. Metabolic diversity in human populations and correlation with genetic and ancestral geographic distances. Mol Genet Metab 2022; 137:292-300. [PMID: 36252453 PMCID: PMC10131177 DOI: 10.1016/j.ymgme.2022.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/04/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022]
Abstract
DNA polymorphic markers and self-defined ethnicity groupings are used to group individuals with shared ancient geographic ancestry. Here we studied whether ancestral relationships between individuals could be identified from metabolic screening data reported by the California newborn screening (NBS) program. NBS data includes 41 blood metabolites measured by tandem mass spectrometry from singleton babies in 17 parent-reported ethnicity groupings. Ethnicity-associated differences identified for 71% of NBS metabolites (29 of 41, Cohen's d > 0.5) showed larger differences in blood levels of acylcarnitines than of amino acids (P < 1e-4). A metabolic distance measure, developed to compare ethnic groupings based on metabolic differences, showed low positive correlation with genetic and ancient geographic distances between the groups' ancestral world populations. Several outlier group pairs were identified with larger genetic and smaller metabolic distances (Black versus White) or with smaller genetic and larger metabolic distances (Chinese versus Japanese) indicating the influence of genetic and of environmental factors on metabolism. Using machine learning, comparison of metabolic profiles between all pairs of ethnic groupings distinguished individuals with larger genetic distance (Black versus Chinese, AUC = 0.96), while genetically more similar individuals could not be separated metabolically (Hispanic versus Native American, AUC = 0.51). Additionally, we identified metabolites informative for inferring metabolic ancestry in individuals from genetically similar populations, which included biomarkers for inborn metabolic disorders (C10:1, C12:1, C3, C5OH, Leucine-Isoleucine). This work sheds new light on metabolic differences in healthy newborns in diverse populations, which could have implications for improving genetic disease screening.
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Affiliation(s)
- Gang Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongyu Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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3
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Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Sci Int Genet 2022; 60:102729. [PMID: 35696960 PMCID: PMC11071123 DOI: 10.1016/j.fsigen.2022.102729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022]
Abstract
A small panel of highly informative loci that can be genotyped on the same equipment as the standard CODIS short tandem repeat (STR) markers has strong potential for application in forensic casework. Single nucleotide polymorphisms (SNPs) can be typed by a couple of methods on capillary electrophoresis (CE) machines and on sequencers, but the amount of information relative to the laboratory effort has hindered use of SNPs in actual casework. Insertion-deletion markers (InDels) suffer from similar problems. Microhaplotypes (MHs) are much more informative per locus but have similar technical difficulties unless they are typed by massively parallel sequencing (MPS). As forensic labs are acquiring sequencing machines, MHs become more likely to be used in casework, especially if multiplexed with STRs. Here we present the details of a multipurpose panel of 24 MHs with the highest effective number of alleles (Ae) from previous work. An augmented STR panel of 24 loci (20 CODIS markers plus four commonly typed STRs) is also considered. The Ae and ancestry informativeness (In) distributions of these two datasets are compared. The MH panel is shown to have better individualization and population distinction than the augmented CODIS STRs. We note that the 24 MHs should be better for mixture analyses than the STRs. Finally, we suggest that a commercial kit including both the standard CODIS markers and this set of 24 MH would greatly improve the discrimination power over that of current commercial assays.
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Affiliation(s)
- Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States.
| | - Andrew J Pakstis
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Neeru Gandotra
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Curt Scharfe
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT 06520, United States
| | - Daniele Podini
- The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC 20007, United States
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4
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Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Sci Rep 2022; 12:7214. [PMID: 35508562 PMCID: PMC9068624 DOI: 10.1038/s41598-022-10706-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA.
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,The Scarborough Hospital, Toronto, ON, Canada
| | - Mustafa Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee On Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, Cerrahpasa, 34500, Istanbul, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
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Mestiri S, Boussetta S, Pakstis AJ, El Kamel S, Ben Ammar El Gaaied A, Kidd KK, Cherni L. New Insight into the human genetic diversity in North African populations by genotyping of
SNPs
in
DRD3
,
CSMD1
and
NRG1
genes. Mol Genet Genomic Med 2022; 10:e1871. [PMID: 35128830 PMCID: PMC8922960 DOI: 10.1002/mgg3.1871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/02/2021] [Accepted: 01/04/2022] [Indexed: 11/06/2022] Open
Abstract
Background The single nucleotide polymorphisms (SNPs) of the dopamine D3 receptor (DRD3), the CUB and sushi multiple domains 1 (CSMD1) and the neuregulin 1 (NRG1) genes were used to study the genetic diversity and affinity among North African populations and to examine their genetic relationships in worldwide populations. Methods The rs3773678, rs3732783 and rs6280 SNPs of the DRD3 gene located on chromosome 3, the rs10108270 SNP of the CSMD1 gene and the rs383632, rs385396 and rs1462906 SNPs of the NRG1 gene located on chromosome 8 were analysed in 366 individuals from seven North African populations (Libya, Kairouan, Mehdia, Sousse, Kesra, Smar and Kerkennah). Results The low values of FST indicated that only 0.27%–1.65% of the genetic variability was due to the differences between the populations. The Kairouan population has the lowest average heterozygosity among the North African populations. Haplotypes composed of the ancestral alleles ACC and ACAT were more frequent in the Kairouan population than in other North African populations. The PCA and the haplotypic analysis showed that the genetic structure of populations in North Africa was closer to that of Europeans, Admixed Americans, South Asians and East Asians. However, analysis of the rs3732783 and rs6280 SNPs revealed that the CT microhaplotype was specific to the North African population. Conclusions The Kairouan population exhibited a relatively low rate of genetic variability. The North African population has undergone significant gene flow but also evolutionary forces that have made it genetically distinct from other populations.
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Affiliation(s)
- Souhir Mestiri
- Laboratory of Genetics, Biodiversity and Bioresource Valorization (LR11ES41) University of Monastir Monastir Tunisia
- Higher Institute of Biotechnology of Monastir Monastir University Monastir Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Andrew J. Pakstis
- Department of Genetics Yale University School of Medicine New Haven Connecticut USA
| | - Sarra El Kamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Amel Ben Ammar El Gaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
| | - Kenneth K. Kidd
- Department of Genetics Yale University School of Medicine New Haven Connecticut USA
| | - Lotfi Cherni
- Higher Institute of Biotechnology of Monastir Monastir University Monastir Tunisia
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis University of Tunis El Manar Tunis Tunisia
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6
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Pakstis AJ, Gandotra N, Speed WC, Murtha M, Scharfe C, Kidd KK. The population genetics characteristics of a 90 locus panel of microhaplotypes. Hum Genet 2021; 140:1753-1773. [PMID: 34643790 PMCID: PMC8553733 DOI: 10.1007/s00439-021-02382-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and small genomic regions with multiple SNPs (microhaplotypes, MHs) are rapidly emerging as novel forensic investigative tools to assist in individual identification, kinship analyses, ancestry inference, and deconvolution of DNA mixtures. Here, we analyzed information for 90 microhaplotype loci in 4009 individuals from 79 world populations in 6 major biogeographic regions. The study included multiplex microhaplotype sequencing (mMHseq) data analyzed for 524 individuals from 16 populations and genotype data for 3485 individuals from 63 populations curated from public repositories. Analyses of the 79 populations revealed excellent characteristics for this 90-plex MH panel for various forensic applications achieving an overall average effective number of allele values (Ae) of 4.55 (range 1.04–19.27) for individualization and mixture deconvolution. Population-specific random match probabilities ranged from a low of 10–115 to a maximum of 10–66. Mean informativeness (In) for ancestry inference was 0.355 (range 0.117–0.883). 65 novel SNPs were detected in 39 of the MHs using mMHseq. Of the 3018 different microhaplotype alleles identified, 1337 occurred at frequencies > 5% in at least one of the populations studied. The 90-plex MH panel enables effective differentiation of population groupings for major biogeographic regions as well as delineation of distinct subgroupings within regions. Open-source, web-based software is available to support validation of this technology for forensic case work analysis and to tailor MH analysis for specific geographical regions.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Neeru Gandotra
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Curt Scharfe
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA.
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7
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Ziadi W, Boussetta S, Elkamel S, Pakstis AJ, Kidd KK, Medimegh I, Ben Ammar Elgaaied A, Cherni L. STAT3 polymorphisms in North Africa and its implication in breast cancer. Mol Genet Genomic Med 2021; 9:e1744. [PMID: 34251094 PMCID: PMC8404238 DOI: 10.1002/mgg3.1744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/28/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Only a few studies have investigated the association of single nucleotide polymorphisms in STAT3 gene with the susceptibility to cancer and response to chemotherapy. Our aim was to determine the allele frequencies of rs3869550, rs957971, and rs7211777 at the STAT3 gene in North African populations and compare them to 1000 genomes populations, and to investigate their relation with cancer. METHODS The targeted SNPs have been analyzed in six Tunisian populations and a sample of Libyans using TaqMan® Assay. The results were compared to 1000 Genomes Project population samples. Targeting of the regions encompassing the three SNPs by micro-ARN was assessed using miR databases. RESULTS The analysis of the 3 SNPs showed that North African populations were close to South Asians. As expected, African populations presented a significant frequency of the ancestral CCG haplotype in contrast to other populations where the fully derived TGA haplotype was more frequent. The presence and diversity of rare haplotypes at STAT3 in North African populations could have been generated by recombination between the two major haplotypes. A screening of the micro-RNA databases showed that the STAT3 region with the mutated allele of rs7211777 (G>A) could be targeted by miR hsa-miR-3606-5p, which also targets genes involved in breast cancer.
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Affiliation(s)
- Wafa Ziadi
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Imen Medimegh
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, Tunisia
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8
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Mestiri S, Boussetta S, Pakstis AJ, Elkamel S, Elgaaied ABA, Kidd KK, Cherni L. Genetic diversity of the North African population revealed by the typing of SNPs in the DRD2/ANKK1 genomic region. Gene 2021; 777:145466. [PMID: 33524518 DOI: 10.1016/j.gene.2021.145466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/11/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
The dopamine - related genes, like dopamine D2 receptor (DRD2) gene and ankyrin repeat and kinase domain containing 1 (ANKK1) gene are implicated in neurological functions. Some polymorphisms of the DRD2/ANKK1 locus (TaqIA, TaqIB, TaqID) have been used to study genetic diversity and the evolution of human populations. The present investigation aims to assess the genetic diversity in seven North African populations in order to explore their genetic structure and to compare them to others worldwide populations studied for the same locus. Nine single nucleotide polymorphisms (SNPs) from the DRD2/ANKK1 locus (rs1800497 TaqIA, rs2242592, rs1124492, rs6277, rs6275, rs1079727, rs2002453, rs2234690 and rs1079597 TaqIB) were typed in 366 individuals from seven North African populations: six from Tunisia (Sousse, Smar, Kesra, Kairouan, Mehdia and Kerkennah) and one from Libya. The allelic frequencies of rs2002453 and rs2234690 were higher in the Smar population than in the other North African populations. More, the Smar population showed the lowest average heterozygosity (0.313). The principal component analysis (PCA) showed that the Smar population was clearly separated from others. Furthermore, linkage disequilibrium analysis shown a high linkage disequilibrium in the North African population and essentially in Smar population. Comparison with other world populations has shown that the heterozygosity of North African population was very close to that of the African and European populations. The PCA and the haplotypic analysis suggested the presence of an important Eurasian genetic component for the North African population. These results suggested that the Smar population was isolated from the others North Africans ones by its peculiar genetic structure because of isolation, endogamy and genetic drift. On the other hand, the North African population is characterized by a multi ancestral gene pool from Eurasia and sub-Saharan Africa due to human migration since prehistoric times.
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Affiliation(s)
- Souhir Mestiri
- Laboratory of Genetics, Biodiversity and Bioresource Valorization (LR11ES41), University of Monastir, Monastir 5000, Tunisia; Higher Institute of Biotechnology of Monastir, Monastir University, 5000 Monastir, Tunisia.
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Lotfi Cherni
- Higher Institute of Biotechnology of Monastir, Monastir University, 5000 Monastir, Tunisia; Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia.
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9
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Mourali-Chebil S, Elkamel S, Boussetta S, Pakstis AJ, Kidd KK, Benammar-Elgaaied A, Cherni L. A Distinctive Pattern of Diversity for the TAS2R38 Gene in North Africa. Hum Biol 2021; 93:163-177. [PMID: 37733614 DOI: 10.1353/hub.2021.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 09/18/2021] [Indexed: 11/11/2022]
Abstract
The TAS2R38 gene is involved in bitter taste perception. This study documents the distinctive diversity patterns in northern Africa of functional single-nucleotide polymorphisms (SNPs) rs713598 and rs1726866 at the TAS2R38 locus and places those patterns in the context of global TAS2R38 diversity. Data previously genotyped with TaqMan assay were analyzed for rs713598 and rs1726866 for 375 unrelated subjects (305 Tunisians from seven locations: Mahdia, Sousse, Kesra, Nebeur, Kairouan, Smar, and Kerkennah; plus 70 Libyans). Data were analyzed to present haplotypes and genotypes before comparison with data from worldwide populations. This study provides information about TAS2R38 diversity in a part of the world that is relatively understudied. Considering the two SNPs rs713598 and rs1726866, the CA nucleotide haplotype leading to the PV amino acid haplotype is extremely rare almost everywhere, but it is relatively frequent (between 6% and 15%) in northern Africa, where it coexists with the globally common amino acid haplotypes PA, AA, and AV. Given its higher frequency in North Africa, the authors propose the CA nucleotide haplotype as a biogeographic marker for forensic purposes.
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Affiliation(s)
- Soufia Mourali-Chebil
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia,
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Andrew J Pakstis
- Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Kenneth K Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
- High Institute of Biotechnology, University of Monastir, Monastir, Tunisia
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10
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Kidd KK, Pakstis AJ, Donnelly MP, Bulbul O, Cherni L, Gurkan C, Kang L, Li H, Yun L, Paschou P, Meiklejohn KA, Haigh E, Speed WC. The distinctive geographic patterns of common pigmentation variants at the OCA2 gene. Sci Rep 2020; 10:15433. [PMID: 32963319 PMCID: PMC7508881 DOI: 10.1038/s41598-020-72262-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/17/2020] [Indexed: 11/25/2022] Open
Abstract
Oculocutaneous Albinism type 2 (OCA2) is a gene of great interest because of genetic variation affecting normal pigmentation variation in humans. The diverse geographic patterns for variant frequencies at OCA2 have been evident but have not been systematically investigated, especially outside of Europe. Here we examine population genetic variation in and near the OCA2 gene from a worldwide perspective. The very different patterns of genetic variation found across world regions suggest strong selection effects may have been at work over time. For example, analyses involving the variants that affect pigmentation of the iris argue that the derived allele of the rs1800407 single nucleotide polymorphism, which produces a hypomorphic protein, may have contributed to the previously demonstrated positive selection in Europe for the enhancer variant responsible for light eye color. More study is needed on the relationships of the genetic variation at OCA2 to variation in pigmentation in areas beyond Europe.
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Affiliation(s)
- Kenneth K Kidd
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA.
| | - Andrew J Pakstis
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
| | - Michael P Donnelly
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA.,Biological and Environmental Sciences, Troy University, Dothan, AL, 36303, USA
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University-Cerrahpasa, Istanbul, 34500, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus), Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Longli Kang
- Key Laboratory forMolecular GeneticMechanisms and Intervention Research On High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China.,Key Laboratory of High Altitude Environment and Genes Related To Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China
| | - Hui Li
- MOE State Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Libing Yun
- Institute of Forensic Medicine, West China College of Preclinical and Forensic Medicine, Sichuan University, No.16. Section 3. RenMin Nan Road, Chengdu, 610041, Sichuan, China
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kelly A Meiklejohn
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Eva Haigh
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
| | - William C Speed
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
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11
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Gu S, Li H, Pakstis AJ, Speed WC, Gurwitz D, Kidd JR, Kidd KK. Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews. Genes (Basel) 2018; 9:genes9090452. [PMID: 30205534 PMCID: PMC6162407 DOI: 10.3390/genes9090452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 12/29/2022] Open
Abstract
The derived human alcohol dehydrogenase (ADH)1B*48His allele of the ADH1B Arg48His polymorphism (rs1229984) has been identified as one component of an East Asian specific core haplotype that underwent recent positive selection. Our study has been extended to Southwest Asia and additional markers in East Asia. Fst values (Sewall Wright’s fixation index) and long-range haplotype analyses identify a strong signature of selection not only in East Asian but also in Southwest Asian populations. However, except for the ADH2B*48His allele, different core haplotypes occur in Southwest Asia compared to East Asia and the extended haplotypes also differ. Thus, the ADH1B*48His allele, as part of a core haplotype of 10 kb, has undergone recent rapid increases in frequency independently in the two regions after divergence of the respective populations. Emergence of agriculture may be the common factor underlying the evident selection.
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Affiliation(s)
- Sheng Gu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Andrew J Pakstis
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - William C Speed
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Judith R Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - Kenneth K Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA.
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12
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Kidd KK, Pakstis AJ, Speed WC, Lagace R, Wootton S, Chang J. Selecting microhaplotypes optimized for different purposes. Electrophoresis 2018; 39:2815-2823. [PMID: 29931757 DOI: 10.1002/elps.201800092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is transforming forensic work by allowing various useful forensic markers, such as STRPs and SNPs, to be multiplexed providing information on ancestry, individual and familial identification, phenotypes for eye/hair/skin pigmentation, and the deconvolution of mixtures. Microhaplotypes also become feasible with massively parallel sequencing, these are DNA segments (smaller than 300 nucleotides) that are selected to contain multiple SNPs unambiguously defining three or more haplotype alleles occurring at common frequencies. The physical extent of a microhaplotype can thus be covered by a single sequence read making these loci phase-known codominant genetic systems. Such microhaplotypes supply significantly more information than a single SNP can. Our efforts to develop useful sets of microhaplotypes have already identified 182 such loci that we have studied on a large number of human populations from around the world. We present various analyses on 83 populations in our ongoing study for a subset of the best microhaplotypes currently available illustrating their characteristics and potential utility for ancestry, identification, and mixture deconvolution.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Lagace
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
| | - Joseph Chang
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
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13
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Kidd KK, Soundararajan U, Rajeevan H, Pakstis AJ, Moore KN, Ropero-Miller JD. The redesigned Forensic Research/Reference on Genetics-knowledge base, FROG-kb. Forensic Sci Int Genet 2018; 33:33-37. [DOI: 10.1016/j.fsigen.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023]
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14
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Bulbul O, Pakstis AJ, Soundararajan U, Gurkan C, Brissenden JE, Roscoe JM, Evsanaa B, Togtokh A, Paschou P, Grigorenko EL, Gurwitz D, Wootton S, Lagace R, Chang J, Speed WC, Kidd KK. Ancestry inference of 96 population samples using microhaplotypes. Int J Legal Med 2017; 132:703-711. [PMID: 29248957 PMCID: PMC5920014 DOI: 10.1007/s00414-017-1748-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022]
Abstract
Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. To provide a better picture of global allele frequency variation, we have now tested 13 more populations for 65 of the microhaplotype loci from among those with higher levels of inter-population gene frequency variation, including 8 loci not previously published. These loci provide clear distinctions among 6 biogeographic regions and provide some information distinguishing up to 10 clusters of populations.
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Affiliation(s)
- Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, 34098, Istanbul, Turkey
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, 99010 (North Cyprus), Nicosia, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, 99628 (North Cyprus), Famagusta, Turkey
| | - Jane E Brissenden
- Department of Medicine, University of Toronto, Toronto, ON, M5S, Canada
| | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, M5S, Canada.,Department of Medicine, The Scarborough Hospital, Toronto, ON, M1P 2V5, Canada
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Khoroo 1, Ulaanbataar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Khoroo 1, Ulaanbataar, Mongolia
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Elena L Grigorenko
- Developmental Cognitive Neuroscience, University of Houston, Houston, TX, 77204, USA.,Laboratory of Translational Sciences of Human Development, St. Petersburg University, St. Petersburg, 199034, Russian Federation
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Robert Lagace
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Joseph Chang
- Human Identification Group, ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA.
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Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: An Allele Frequency Database for Microevolutionary Studies. Evol Bioinform Online 2017. [DOI: 10.1177/117693430500100006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kei-Hoi Cheung
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Rohit Gadagkar
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Shannon Stein
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Perry L Miller
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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16
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Cherni L, Pakstis AJ, Boussetta S, Elkamel S, Frigi S, Khodjet-El-Khil H, Barton A, Haigh E, Speed WC, Ben Ammar Elgaaied A, Kidd JR, Kidd KK. Genetic variation in Tunisia in the context of human diversity worldwide. Am J Phys Anthropol 2016; 161:62-71. [PMID: 27192181 PMCID: PMC5084816 DOI: 10.1002/ajpa.23008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 04/22/2016] [Indexed: 11/09/2022]
Abstract
OBJECTIVES North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context. MATERIALS AND METHODS Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses. RESULTS Average heterozygosity of the North African populations is high relative to our global samples, consistent with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found. DISCUSSION Known historical migrations and invasions did not displace or homogenize the genetic variation in the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future studies across North Africa have the potential to increase our understanding of the historical demographic factors influencing the region. Am J Phys Anthropol 161:62-71, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Sabeh Frigi
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Alison Barton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Amel Ben Ammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520
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17
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Boyden SE, Desai A, Cruse G, Young ML, Bolan HC, Scott LM, Eisch AR, Long RD, Lee CCR, Satorius CL, Pakstis AJ, Olivera A, Mullikin JC, Chouery E, Mégarbané A, Medlej-Hashim M, Kidd KK, Kastner DL, Metcalfe DD, Komarow HD. Vibratory Urticaria Associated with a Missense Variant in ADGRE2. N Engl J Med 2016; 374:656-63. [PMID: 26841242 PMCID: PMC4782791 DOI: 10.1056/nejmoa1500611] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Patients with autosomal dominant vibratory urticaria have localized hives and systemic manifestations in response to dermal vibration, with coincident degranulation of mast cells and increased histamine levels in serum. We identified a previously unknown missense substitution in ADGRE2 (also known as EMR2), which was predicted to result in the replacement of cysteine with tyrosine at amino acid position 492 (p.C492Y), as the only nonsynonymous variant cosegregating with vibratory urticaria in two large kindreds. The ADGRE2 receptor undergoes autocatalytic cleavage, producing an extracellular subunit that noncovalently binds a transmembrane subunit. We showed that the variant probably destabilizes an autoinhibitory subunit interaction, sensitizing mast cells to IgE-independent vibration-induced degranulation. (Funded by the National Institutes of Health.).
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Affiliation(s)
- Steven E Boyden
- From the Inflammatory Disease Section, National Human Genome Research Institute (S.E.B., C.L.S., D.L.K.), Mast Cell Biology Section, National Institute of Allergy and Infectious Diseases, (A.D., G.C., H.C.B., L.M.S., A.R.E., A.O., D.D.M., H.D.K.), Laboratory of Pathology, National Cancer Institute (C.-C.R.L.), and National Institutes of Health (NIH) Intramural Sequencing Center, National Human Genome Research Institute (J.C.M.), NIH, Bethesda, and Clinical Research Directorate-Clinical Monitoring Research Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick (M.L.Y.) - both in Maryland; Veterinary Pathology Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT (R.D.L.); the Department of Genetics, Yale University School of Medicine, New Haven, CT (A.J.P., K.K.K.); Medical Genetics Unit, Saint Joseph University, Beirut (E.C.) and Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Fanar (M.M.-H.) - both in Lebanon; and Institut Jérôme Lejeune, Paris (A.M.)
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18
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Pakstis AJ, Haigh E, Cherni L, ElGaaied ABA, Barton A, Evsanaa B, Togtokh A, Brissenden J, Roscoe J, Bulbul O, Filoglu G, Gurkan C, Meiklejohn KA, Robertson JM, Li CX, Wei YL, Li H, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. 52 additional reference population samples for the 55 AISNP panel. Forensic Sci Int Genet 2015; 19:269-271. [DOI: 10.1016/j.fsigen.2015.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 12/31/2022]
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19
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Yu D, Mathews CA, Scharf JM, Neale BM, Davis LK, Gamazon ER, Derks EM, Evans P, Edlund CK, Crane J, Fagerness JA, Osiecki L, Gallagher P, Gerber G, Haddad S, Illmann C, McGrath LM, Mayerfeld C, Arepalli S, Barlassina C, Barr CL, Bellodi L, Benarroch F, Berrió GB, Bienvenu OJ, Black D, Bloch MH, Brentani H, Bruun RD, Budman CL, Camarena B, Campbell DD, Cappi C, Cardona Silgado JC, Cavallini MC, Chavira DA, Chouinard S, Cook EH, Cookson MR, Coric V, Cullen B, Cusi D, Delorme R, Denys D, Dion Y, Eapen V, Egberts K, Falkai P, Fernandez T, Fournier E, Garrido H, Geller D, Gilbert D, Girard SL, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Grünblatt E, Hardy J, Heiman GA, Hemmings SM, Herrera LD, Hezel DM, Hoekstra PJ, Jankovic J, Kennedy JL, King RA, Konkashbaev AI, Kremeyer B, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Liu C, Lochner C, Lowe TL, Lupoli S, Macciardi F, Maier W, Manunta P, Marconi M, McCracken JT, Mesa Restrepo SC, Moessner R, Moorjani P, Morgan J, Muller H, Murphy DL, Naarden AL, Ochoa WC, Ophoff RA, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Rauch SL, Renner T, Reus VI, Richter MA, Riddle MA, Robertson MM, Romero R, Rosário MC, Rosenberg D, Ruhrmann S, Sabatti C, Salvi E, Sampaio AS, Samuels J, Sandor P, Service SK, Sheppard B, Singer HS, Smit JH, Stein DJ, Strengman E, Tischfield JA, Turiel M, Valencia Duarte AV, Vallada H, Veenstra-VanderWeele J, Walitza S, Walkup J, Wang Y, Weale M, Weiss R, Wendland JR, Westenberg HG, Yao Y, Hounie AG, Miguel EC, Nicolini H, Wagner M, Ruiz-Linares A, Cath DC, McMahon W, Posthuma D, Oostra BA, Nestadt G, Rouleau GA, Purcell S, Jenike MA, Heutink P, Hanna GL, Conti DV, Arnold PD, Freimer N, Stewart SE, Knowles JA, Cox NJ, Pauls DL. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD. Am J Psychiatry 2015; 172:82-93. [PMID: 25158072 PMCID: PMC4282594 DOI: 10.1176/appi.ajp.2014.13101306] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The authors report a combined genome-wide association study (GWAS) of Tourette's syndrome and OCD. METHOD The authors conducted a GWAS in 2,723 cases (1,310 with OCD, 834 with Tourette's syndrome, 579 with OCD plus Tourette's syndrome/chronic tics), 5,667 ancestry-matched controls, and 290 OCD parent-child trios. GWAS summary statistics were examined for enrichment of functional variants associated with gene expression levels in brain regions. Polygenic score analyses were conducted to investigate the genetic architecture within and across the two disorders. RESULTS Although no individual single-nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels (expression quantitative loci, or eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10(-4)), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, Tourette's syndrome had a smaller, nonsignificant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and co-occurring Tourette's syndrome/chronic tics were included in the analysis (p=0.01). CONCLUSIONS Previous work has shown that Tourette's syndrome and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct components to the genetic architectures of these two disorders. Furthermore, OCD with co-occurring Tourette's syndrome/chronic tics may have different underlying genetic susceptibility compared with OCD alone.
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Affiliation(s)
- Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Co-corresponding authors: Dongmei Yu, MS & David L. Pauls, Ph.D., Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Simches Research Building, 6th Floor, 185 Cambridge Street, Boston, MA 02114
| | - Carol A. Mathews
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Jeremiah M. Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA,Division of Cognitive and Behavioral Neurology, Brigham and Womens Hospital, Boston, MA, USA
| | - Benjamin M. Neale
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lea K. Davis
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Eske M. Derks
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick Evans
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Christopher K. Edlund
- Department of Preventative Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jacquelyn Crane
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesen A. Fagerness
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Patience Gallagher
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gloria Gerber
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen Haddad
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren M. McGrath
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Catherine Mayerfeld
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Cristina Barlassina
- Genomic and Bioinformatic Unit, Filarete Foundation, Milano, Italy,Department of Health Sciences, Graduate School of Nephrology, University of Milano
| | - Cathy L. Barr
- The Toronto Western Research Institute, University Health Network, Toronto, ON, Canada,The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Fortu Benarroch
- Herman Dana Division of Child and Adolescent Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - O. Joseph Bienvenu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Donald Black
- Department of Psychiatry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael H. Bloch
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Helena Brentani
- Department of Psychiatry, University of São Paulo Medical School, Brazil
| | - Ruth D. Bruun
- North Shore-Long Island Jewish Medical Center, Manhasset, NY, USA,New York University Medical Center, New York, NY, USA
| | - Cathy L. Budman
- North Shore-Long Island Jewish Health System, Manhasset, NY, USA,Hofstra University School of Medicine, Hempstead, NY, USA
| | - Beatriz Camarena
- Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico City, Mexico
| | - Desmond D. Campbell
- University College London, London, UK,Department of Psychiatry, University of Hong Kong, Hong Kong
| | - Carolina Cappi
- Department of Psychiatry, University of São Paulo Medical School, Brazil
| | | | | | - Denise A. Chavira
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Psychology, University of California Los Angeles, Los Angeles, CA, USA
| | - Sylvain Chouinard
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, USA
| | - M. R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir Coric
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bernadette Cullen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniele Cusi
- Genomic and Bioinformatic Unit, Filarete Foundation, Milano, Italy,Department of Health Sciences, Graduate School of Nephrology, University of Milano
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France,Foundation Fondamental, French National Science Foundation, France,AP-HP, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | - Damiaan Denys
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands,Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Yves Dion
- Department of Psychiatry, University of Montreal, Montreal, Quebec, Canada
| | - Valsama Eapen
- Infant Child and Adolescent Psychiatry, University of New South Wales, Australia,Academic Unit of Child Psychiatry, South West Sydney LHD (AUCS), Australia
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Thomas Fernandez
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Helena Garrido
- Clinica Herrera Amighetti, Avenida Escazú, San José, Costa Rica
| | - Daniel Geller
- OCD Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Donald Gilbert
- Cincinnati Children’s Hospital Medical Center and the University of Cincinnati, Cincinnati, OH, USA
| | - Simon L. Girard
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, Helios-Hospital Stralsund, University Medicine Greifswald, Greifswald, Germany
| | - Marco A. Grados
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benjamin D. Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Providence, Rhode Island, USA
| | - Varda Gross-Tsur
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry, University of Zurich, Zurich, Switzerland
| | | | - Gary A. Heiman
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, US
| | - Sian M.J. Hemmings
- Department of Psychiatry, University of Stellenbosch, Stellenbosch, South Africa
| | | | - Dianne M. Hezel
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Pieter J. Hoekstra
- Department of Psychiatry, University Medical Center, University of Groningen, Groningen, The Netherlands
| | - Joseph Jankovic
- Parkinson’s Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - James L. Kennedy
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Canada,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Robert A. King
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Anuar I. Konkashbaev
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Roger Kurlan
- Atlantic Neuroscience Institute, Overlook Hospital, Summit, NJ, USA
| | | | - Marion Leboyer
- Foundation Fondamental, French National Science Foundation, France,AP-HP, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France,Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, Créteil, F 94000, France
| | - James F. Leckman
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Leonhard Lennertz
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Chunyu Liu
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Christine Lochner
- MRC Unit on Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Stellenbosch, South Africa
| | - Thomas L. Lowe
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Sara Lupoli
- Genomic and Bioinformatic Unit, Filarete Foundation, Milano, Italy,Department of Health Sciences, Graduate School of Nephrology, University of Milano
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, School of Medicine, University of California Irvine (UCI), California, USA
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Paolo Manunta
- Division of Nephrology and Dialysis, San Raffaele Scientific Institute - Chair of Nephrology, Università Vita Salute San Raffaele, Milan, Italy
| | - Maurizio Marconi
- Center of Transfusion Medicine and Immunohematology, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - James T. McCracken
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, David Geffen School of Medicine, California, USA
| | | | - Rainald Moessner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Priya Moorjani
- Department of Genetics, Harvard University, Cambridge, MA, USA
| | | | | | - Dennis L. Murphy
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda, MD, USA
| | - Allan L. Naarden
- Department of Clinical Research, Medical City Dallas Hospital, Dallas, Texas, USA
| | | | - Roel A. Ophoff
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center, Utrecht, The Netherlands,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrew J. Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Michele T. Pato
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Carlos N. Pato
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John Piacentini
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, David Geffen School of Medicine, California, USA
| | - Christopher Pittenger
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yehuda Pollak
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Scott L. Rauch
- Partners Psychiatry and McLean Hospital, Boston, MA, USA
| | - Tobias Renner
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Germany
| | - Victor I. Reus
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Margaret A. Richter
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada,Frederick W. Thompson Anxiety Disorders Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Mark A. Riddle
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Maria C. Rosário
- Child and Adolescent Psychiatry Unit (UPIA), Department of Psychiatry, Federal University of São Paulo, Brazil
| | - David Rosenberg
- Department of Psychiatry & Behavioral Neurosciences, Wayne State University and the Detroit Medical Center
| | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Chiara Sabatti
- Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Erika Salvi
- Genomic and Bioinformatic Unit, Filarete Foundation, Milano, Italy,Department of Health Sciences, Graduate School of Nephrology, University of Milano
| | - Aline S. Sampaio
- University Health Care Services - SMURB, Universidade Federal da Bahia, Salvador, Bahia, Brazil,Department of Psychiatry, Faculdade de Medicina da Universidade de Sao Paulo, Brazil
| | - Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Paul Sandor
- Department of Psychiatry, University of Toronto and University Health Network, Toronto Western Research Institute and Youthdale Treatment Centers, Toronto, Ontario, Canada
| | - Susan K. Service
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Brooke Sheppard
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | | | - Jan H. Smit
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Dan J. Stein
- University of Cape Town, Cape Town, South Africa
| | - Eric Strengman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jay A. Tischfield
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, US
| | - Maurizio Turiel
- Department of Health Technologies, University of Milano, Milano, Italy
| | | | - Homero Vallada
- Department of Psychiatry, University of São Paulo Medical School, Brazil
| | - Jeremy Veenstra-VanderWeele
- Departments of Psychiatry, Pediatrics, and Pharmacology, Kennedy Center for Research on Human Development, and Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry, University of Zurich, Zurich, Switzerland,Department of Child and Adolescent Psychiatry, University of Würzburg, Germany
| | - John Walkup
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Weill Cornell Medical Center, New York, NY, USA
| | - Ying Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mike Weale
- Department of Medical & Molecular Genetics, King’s College London, UK
| | | | - Jens R. Wendland
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda, MD, USA
| | - Herman G.M. Westenberg
- Department of Psychiatry, Academic Medical Center and Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Yin Yao
- Unit on Statistical Genomics, NIMH Intramural Research Program, Bethesda, MD, USA
| | - Ana G. Hounie
- Department of Psychiatry, Faculdade de Medicina da Universidade de Sao Paulo, Brazil
| | | | | | - Michael Wagner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | | | - Danielle C. Cath
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands,Department of Clinical & Health Psychology, Utrecht University, Utrecht, The Netherlands
| | - William McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
| | - Danielle Posthuma
- Section of Medical Genomics, Department of Clinical Genetics, VU University Medical Center Amsterdam, The Netherlands,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan Amsterdam, The Netherlands,Department of Child and Adolescent Psychiatry, Erasmus University Medical Centre, Wytemaweg 8, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Shaun Purcell
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Mt. Sinai Medical Center, New York, NY, USA
| | - Michael A. Jenike
- OCD Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Peter Heutink
- Section of Medical Genomics, Department of Clinical Genetics, VU University Medical Center Amsterdam, The Netherlands,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Gregory L. Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - David V. Conti
- Department of Preventative Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Paul D. Arnold
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - S. Evelyn Stewart
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,British Columbia Mental Health and Addictions Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - James A. Knowles
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - David L. Pauls
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Co-corresponding authors: Dongmei Yu, MS & David L. Pauls, Ph.D., Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Simches Research Building, 6th Floor, 185 Cambridge Street, Boston, MA 02114
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20
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McGrath LM, Yu D, Marshall C, Davis LK, Thiruvahindrapuram B, Li B, Cappi C, Gerber G, Wolf A, Schroeder FA, Osiecki L, O'Dushlaine C, Kirby A, Illmann C, Haddad S, Gallagher P, Fagerness JA, Barr CL, Bellodi L, Benarroch F, Bienvenu OJ, Black DW, Bloch MH, Bruun RD, Budman CL, Camarena B, Cath DC, Cavallini MC, Chouinard S, Coric V, Cullen B, Delorme R, Denys D, Derks EM, Dion Y, Rosário MC, Eapen V, Evans P, Falkai P, Fernandez TV, Garrido H, Geller D, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Grünblatt E, Heiman GA, Hemmings SMJ, Herrera LD, Hounie AG, Jankovic J, Kennedy JL, King RA, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Lochner C, Lowe TL, Lyon GJ, Macciardi F, Maier W, McCracken JT, McMahon W, Murphy DL, Naarden AL, Neale BM, Nurmi E, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Reus VI, Richter MA, Riddle M, Robertson MM, Rosenberg D, Rouleau GA, Ruhrmann S, Sampaio AS, Samuels J, Sandor P, Sheppard B, Singer HS, Smit JH, Stein DJ, Tischfield JA, Vallada H, Veenstra-VanderWeele J, Walitza S, Wang Y, Wendland JR, Shugart YY, Miguel EC, Nicolini H, Oostra BA, Moessner R, Wagner M, Ruiz-Linares A, Heutink P, Nestadt G, Freimer N, Petryshen T, Posthuma D, Jenike MA, Cox NJ, Hanna GL, Brentani H, Scherer SW, Arnold PD, Stewart SE, Mathews CA, Knowles JA, Cook EH, Pauls DL, Wang K, Scharf JM. Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study. J Am Acad Child Adolesc Psychiatry 2014; 53:910-9. [PMID: 25062598 PMCID: PMC4218748 DOI: 10.1016/j.jaac.2014.04.022] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/16/2014] [Accepted: 06/18/2014] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Obsessive-compulsive disorder (OCD) and Tourette syndrome (TS) are heritable neurodevelopmental disorders with a partially shared genetic etiology. This study represents the first genome-wide investigation of large (>500 kb), rare (<1%) copy number variants (CNVs) in OCD and the largest genome-wide CNV analysis in TS to date. METHOD The primary analyses used a cross-disorder design for 2,699 case patients (1,613 ascertained for OCD, 1,086 ascertained for TS) and 1,789 controls. Parental data facilitated a de novo analysis in 348 OCD trios. RESULTS Although no global CNV burden was detected in the cross-disorder analysis or in secondary, disease-specific analyses, there was a 3.3-fold increased burden of large deletions previously associated with other neurodevelopmental disorders (p = .09). Half of these neurodevelopmental deletions were located in a single locus, 16p13.11 (5 case patient deletions: 0 control deletions, p = .08 in the current study, p = .025 compared to published controls). Three 16p13.11 deletions were confirmed de novo, providing further support for the etiological significance of this region. The overall OCD de novo rate was 1.4%, which is intermediate between published rates in controls (0.7%) and in individuals with autism or schizophrenia (2-4%). CONCLUSION Several converging lines of evidence implicate 16p13.11 deletions in OCD, with weaker evidence for a role in TS. The trend toward increased overall neurodevelopmental CNV burden in TS and OCD suggests that deletions previously associated with other neurodevelopmental disorders may also contribute to these phenotypes.
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Affiliation(s)
- Lauren M McGrath
- Massachusetts General Hospital, Boston; American University, Washington, DC; Harvard-MIT Broad Institute, Boston
| | - Dongmei Yu
- Massachusetts General Hospital, Boston; Harvard-MIT Broad Institute, Boston
| | | | | | | | - Bingbin Li
- University of Toronto and the Hospital for Sick Children, Toronto
| | | | | | | | | | | | | | | | | | | | | | | | - Cathy L Barr
- University of Toronto and the Hospital for Sick Children, Toronto; Toronto Western Research Institute, University Health Network, Toronto
| | | | | | | | | | | | - Ruth D Bruun
- North Shore-Long Island Jewish Medical Center, New Hyde Park, NY; New York University Medical Center, New York
| | - Cathy L Budman
- North Shore-Long Island Jewish Medical Center, New Hyde Park, NY; Hofstra University School of Medicine, Hempstead, NY
| | - Beatriz Camarena
- Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico
| | | | | | | | | | | | - Richard Delorme
- Robert Debre University Hospital, Paris and the French National Science Foundation, Creteil, France; Institut Pasteur, Paris
| | - Damiaan Denys
- Netherlands Institute for Neuroscience, Amsterdam; Academic Medical Center, Amsterdam
| | | | | | | | | | | | | | | | - Helena Garrido
- Hospital Nacional de Niños, San Jose, Costa Rica; Clinica Herrera Amighetti, Avenida Escazú, San José, Costa Rica
| | | | - Hans J Grabe
- University Medicine Greifswald, Greifswald, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marion Leboyer
- Robert Debre University Hospital, Paris and the French National Science Foundation, Creteil, France; Institut Mondor de Recherche Biomédicale, Créteil, France
| | | | | | | | - Thomas L Lowe
- University of California at San Francisco School of Medicine
| | | | | | | | | | | | - Dennis L Murphy
- National Institute of Mental Health (NIMH) Intramural Research Program, Bethesda, MD
| | | | - Benjamin M Neale
- Massachusetts General Hospital, Boston; Harvard-MIT Broad Institute, Boston
| | - Erika Nurmi
- University of California, Los Angeles (UCLA) School of Medicine
| | | | | | | | - John Piacentini
- University of California, Los Angeles (UCLA) School of Medicine
| | | | | | - Victor I Reus
- University of California at San Francisco School of Medicine
| | - Margaret A Richter
- University of Toronto and the Hospital for Sick Children, Toronto; Sunnybrook Health Sciences Centre, Toronto
| | - Mark Riddle
- Johns Hopkins University School of Medicine, Baltimore
| | | | | | | | | | - Aline S Sampaio
- Federal University of São Paulo; Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Jack Samuels
- Johns Hopkins University School of Medicine, Baltimore
| | - Paul Sandor
- University of Toronto and the Hospital for Sick Children, Toronto; Toronto Western Research Institute, University Health Network, Toronto
| | - Brooke Sheppard
- University of California at San Francisco School of Medicine
| | | | - Jan H Smit
- VU Amsterdam and Erasmus University Medical Centre, Rotterdam; VU University Amsterdam; VU Medical Center, Amsterdam
| | | | | | | | | | | | - Ying Wang
- Johns Hopkins University School of Medicine, Baltimore
| | - Jens R Wendland
- National Institute of Mental Health (NIMH) Intramural Research Program, Bethesda, MD
| | - Yin Yao Shugart
- National Institute of Mental Health (NIMH) Intramural Research Program, Bethesda, MD
| | | | | | - Ben A Oostra
- Erasmus Medical Center Rotterdam, the Netherlands
| | | | | | | | - Peter Heutink
- German Center for Neurodegenerative Diseases, Bonn and VU Medical Center Amsterdam
| | | | - Nelson Freimer
- University of California, Los Angeles (UCLA) School of Medicine; Semel Institute for Neuroscience and Human Behavior, UCLA
| | - Tracey Petryshen
- Massachusetts General Hospital, Boston; Harvard-MIT Broad Institute, Boston
| | | | | | | | | | | | | | - Paul D Arnold
- University of Toronto and the Hospital for Sick Children, Toronto
| | - S Evelyn Stewart
- Massachusetts General Hospital, Boston; University of British Columbia, Vancouver
| | - Carol A Mathews
- University of California at San Francisco School of Medicine
| | | | | | | | - Kai Wang
- Zilkha Neurogenetic Institute, Los Angeles
| | - Jeremiah M Scharf
- Massachusetts General Hospital, Boston; Brigham and Womens Hospital, Boston; Harvard-MIT Broad Institute, Boston.
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21
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Kidd KK, Pakstis AJ, Speed WC, Lagacé R, Chang J, Wootton S, Haigh E, Kidd JR. Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics. Forensic Sci Int Genet 2014; 12:215-24. [PMID: 25038325 DOI: 10.1016/j.fsigen.2014.06.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/01/2014] [Accepted: 06/23/2014] [Indexed: 11/24/2022]
Abstract
SNPs that are molecularly very close (<10kb) will generally have extremely low recombination rates, much less than 10(-4). Multiple haplotypes will often exist because of the history of the origins of the variants at the different sites, rare recombinants, and the vagaries of random genetic drift and/or selection. Such multiallelic haplotype loci are potentially important in forensic work for individual identification, for defining ancestry, and for identifying familial relationships. The new DNA sequencing capabilities currently available make possible continuous runs of a few hundred base pairs so that we can now determine the allelic combination of multiple SNPs on each chromosome of an individual, i.e., the phase, for multiple SNPs within a small segment of DNA. Therefore, we have begun to identify regions, encompassing two to four SNPs with an extent of <200bp that define multiallelic haplotype loci. We have identified candidate regions and have collected pilot data on many candidate microhaplotype loci. Here we present 31 microhaplotype loci that have at least three alleles, have high heterozygosity, are globally informative, and are statistically independent at the population level. This study of microhaplotype loci (microhaps) provides proof of principle that such markers exist and validates their usefulness for ancestry inference, lineage-clan-family inference, and individual identification. The true value of microhaplotypes will come with sequencing methods that can establish alleles unambiguously, including disentangling of mixtures, because a single sequencing run on a single strand of DNA will encompass all of the SNPs.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Joseph Chang
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Sharon Wootton
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Eva Haigh
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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22
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Murdoch JD, Speed WC, Pakstis AJ, Heffelfinger CE, Kidd KK. Worldwide population variation and haplotype analysis at the serotonin transporter gene SLC6A4 and implications for association studies. Biol Psychiatry 2013; 74:879-89. [PMID: 23510579 DOI: 10.1016/j.biopsych.2013.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 11/28/2012] [Accepted: 02/11/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Variation at the serotonin transporter gene, SLC6A4, has been associated with a variety of neuropsychiatric disorders and could be involved in other health-related phenotypes. METHODS To determine the extent of variation at SLC6A4, we genotyped 23 markers on approximately 2500 individuals from 47 global populations, including the promoter variable number tandem repeat (VNTR) and 2 single nucleotide polymorphisms (SNPs) immediately flanking its variable region (rs25531 and rs25532), the intron 2 VNTR, and 19 additional SNPs. RESULTS We observed several rare alleles at the promoter VNTR (some novel) and population-specific distributions of the reported functional SNPs rs25531, rs25532, and rs6355, as well as two alleles at the intron 2 VNTR. Alleles of interest at the VNTRs occurred on specific haplotype backgrounds. The repeat-number variants at the promoter VNTR and the intron 2 VNTR, as well as the putative functional SNPs, showed ethnic variation in frequencies. The more common alleles at the VNTR polymorphisms show wide geographic distributions, whereas rare alleles at both show more restricted distributions. The derived alleles at the two functional SNPs in the promoter VNTR show restricted distributions and occur primarily on different repeat number alleles. CONCLUSIONS Our findings illustrate significant variation worldwide at SLC6A4 and that the functionally implicated alleles at the SNPs rs25531, rs25532, and rs6355 occur on limited haplotypes and vary significantly in global distribution. Association studies at SLC6A4 cannot a priori extrapolate across populations and should account for the multiple polymorphisms with possible functional variation across this locus, rather than focusing solely on one or two polymorphisms as commonly seen.
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Affiliation(s)
- John D Murdoch
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.
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Kidd KK, Pakstis AJ, Yun L. An historical perspective on "The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus". Hum Genet 2013; 133:431-3. [PMID: 24162668 DOI: 10.1007/s00439-013-1386-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 10/19/2013] [Indexed: 10/26/2022]
Abstract
Human population genetics is a completely different science today compared to two decades ago, at least at the empiric level. Our paper [Chang (Hum Genet 98:91-101, 1996a)] demonstrated that three different alleles were common when one considered many populations although other low frequency alleles occurred. Because previous work had been largely done on European subjects, our findings involved 36 distinct populations and showed that East Asian populations had nearly lost the 7-repeat allele, and that Native American populations had the highest frequencies of that allele globally, was a significant early empiric demonstration of the potential magnitude of population variation at important genes. There are thousands of loci tested on many of the same populations and the gene frequency pattern seen for the DRD4 7-repeat allele is seen at other loci, arguing that this pattern commonly reflects the pattern of divergence of populations and accumulated random genetic drift.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, PO Box 208005, New Haven, CT, 06520-8005, USA,
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24
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Davis LK, Yu D, Keenan CL, Gamazon ER, Konkashbaev AI, Derks EM, Neale BM, Yang J, Lee SH, Evans P, Barr CL, Bellodi L, Benarroch F, Berrio GB, Bienvenu OJ, Bloch MH, Blom RM, Bruun RD, Budman CL, Camarena B, Campbell D, Cappi C, Cardona Silgado JC, Cath DC, Cavallini MC, Chavira DA, Chouinard S, Conti DV, Cook EH, Coric V, Cullen BA, Deforce D, Delorme R, Dion Y, Edlund CK, Egberts K, Falkai P, Fernandez TV, Gallagher PJ, Garrido H, Geller D, Girard SL, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Haddad S, Heiman GA, Hemmings SMJ, Hounie AG, Illmann C, Jankovic J, Jenike MA, Kennedy JL, King RA, Kremeyer B, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Liu C, Lochner C, Lowe TL, Macciardi F, McCracken JT, McGrath LM, Mesa Restrepo SC, Moessner R, Morgan J, Muller H, Murphy DL, Naarden AL, Ochoa WC, Ophoff RA, Osiecki L, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Rauch SL, Renner TJ, Reus VI, Richter MA, Riddle MA, Robertson MM, Romero R, Rosàrio MC, Rosenberg D, Rouleau GA, Ruhrmann S, Ruiz-Linares A, Sampaio AS, Samuels J, Sandor P, Sheppard B, Singer HS, Smit JH, Stein DJ, Strengman E, Tischfield JA, Valencia Duarte AV, Vallada H, Van Nieuwerburgh F, Veenstra-VanderWeele J, Walitza S, Wang Y, Wendland JR, Westenberg HGM, Shugart YY, Miguel EC, McMahon W, Wagner M, Nicolini H, Posthuma D, Hanna GL, Heutink P, Denys D, Arnold PD, Oostra BA, Nestadt G, Freimer NB, Pauls DL, Wray NR, Stewart SE, Mathews CA, Knowles JA, Cox NJ, Scharf JM. Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. PLoS Genet 2013; 9:e1003864. [PMID: 24204291 PMCID: PMC3812053 DOI: 10.1371/journal.pgen.1003864] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
The direct estimation of heritability from genome-wide common variant data as implemented in the program Genome-wide Complex Trait Analysis (GCTA) has provided a means to quantify heritability attributable to all interrogated variants. We have quantified the variance in liability to disease explained by all SNPs for two phenotypically-related neurobehavioral disorders, obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS), using GCTA. Our analysis yielded a heritability point estimate of 0.58 (se = 0.09, p = 5.64e-12) for TS, and 0.37 (se = 0.07, p = 1.5e-07) for OCD. In addition, we conducted multiple genomic partitioning analyses to identify genomic elements that concentrate this heritability. We examined genomic architectures of TS and OCD by chromosome, MAF bin, and functional annotations. In addition, we assessed heritability for early onset and adult onset OCD. Among other notable results, we found that SNPs with a minor allele frequency of less than 5% accounted for 21% of the TS heritability and 0% of the OCD heritability. Additionally, we identified a significant contribution to TS and OCD heritability by variants significantly associated with gene expression in two regions of the brain (parietal cortex and cerebellum) for which we had available expression quantitative trait loci (eQTLs). Finally we analyzed the genetic correlation between TS and OCD, revealing a genetic correlation of 0.41 (se = 0.15, p = 0.002). These results are very close to previous heritability estimates for TS and OCD based on twin and family studies, suggesting that very little, if any, heritability is truly missing (i.e., unassayed) from TS and OCD GWAS studies of common variation. The results also indicate that there is some genetic overlap between these two phenotypically-related neuropsychiatric disorders, but suggest that the two disorders have distinct genetic architectures.
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Affiliation(s)
- Lea K. Davis
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (LKD); (JMS)
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Clare L. Keenan
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Anuar I. Konkashbaev
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Eske M. Derks
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Benjamin M. Neale
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jian Yang
- The University of Queensland, Diamantina Institute, Queensland, Australia
- The University of Queensland, Queensland Brain Institute, Queensland, Australia
| | - S. Hong Lee
- The University of Queensland, Queensland Brain Institute, Queensland, Australia
| | - Patrick Evans
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Cathy L. Barr
- The Toronto Western Research Institute, University Health Network, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Fortu Benarroch
- Herman Dana Division of Child and Adolescent Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Oscar J. Bienvenu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michael H. Bloch
- Department of Psychiatry, Yale University, New Haven, Connecticut, United States of America
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Rianne M. Blom
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth D. Bruun
- North Shore-Long Island Jewish Medical Center, Manhasset, New York, United States of America
- New York University Medical Center, New York, New York, United States of America
| | - Cathy L. Budman
- North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
- Hofstra University School of Medicine, Hempstead, New York, United States of America
| | - Beatriz Camarena
- Instituto Nacional de Psiquiatría Ramon de la Fuente Muñiz, Mexico City, Mexico
| | - Desmond Campbell
- University College London, London, United Kingdom
- Department of Psychiatry, University of Hong Kong, Hong Kong, China
| | - Carolina Cappi
- Department of Psychiatry, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Danielle C. Cath
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
- Department of Clinical & Health Psychology, Utrecht University, Utrecht, The Netherlands
- Altrecht Academic Anxiety Center, Utrecht, The Netherlands
| | | | - Denise A. Chavira
- Department of Psychology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | | | - David V. Conti
- Department of Preventative Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Vladimir Coric
- Department of Psychiatry, Yale University, New Haven, Connecticut, United States of America
| | - Bernadette A. Cullen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- Fondation Fondamental, French National Science Foundation, Creteil, France
- AP-HP, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | - Yves Dion
- Department of Psychiatry, University of Montreal, Montreal, Quebec, Canada
| | - Christopher K. Edlund
- Department of Preventative Medicine, Division of Biostatistics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Karin Egberts
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University of Munich, Munich, Germany
| | - Thomas V. Fernandez
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Patience J. Gallagher
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Helena Garrido
- Clinica Herrera Amighetti, Avenida Escazú, San José, Costa Rica
| | - Daniel Geller
- OCD Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, Helios-Hospital Stralsund, University Medicine Greifswald, Greifswald, Germany
| | - Marco A. Grados
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Benjamin D. Greenberg
- Department of Psychiatry and Human Behavior, Brown Medical School, Butler Hospital, Providence, Rhode Island, United States of America
| | - Varda Gross-Tsur
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Stephen Haddad
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gary A. Heiman
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
| | - Sian M. J. Hemmings
- Department of Psychiatry, University of Stellenbosch, Stellenbosch, South Africa
| | - Ana G. Hounie
- Department of Psychiatry, Faculdade de Medicina da Universidade de Säo Paulo, Brazil
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael A. Jenike
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - James L. Kennedy
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Robert A. King
- Yale Child Study Center, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | | | - Roger Kurlan
- Atlantic Neuroscience Institute, Overlook Hospital, Summit, New Jersey, United States of America
| | | | - Marion Leboyer
- Fondation Fondamental, French National Science Foundation, Creteil, France
- AP-HP, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
- Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, Créteil, France
| | - James F. Leckman
- Child Study Center, Psychiatry, Pediatrics and Psychology, Yale University, New Haven, Connecticut, United States of America
| | - Leonhard Lennertz
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Chunyu Liu
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Christine Lochner
- MRC Unit on Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Stellenbosch, South Africa
| | - Thomas L. Lowe
- Department of Psychiatry, University of California at San Francisco, San Francisco, California, United States of America
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, School of Medicine, University of California Irvine (UCI), Irvine, California, United States of America
| | - James T. McCracken
- Department of Psychiatry and Human Behavior, School of Medicine, University of California Irvine (UCI), Irvine, California, United States of America
| | - Lauren M. McGrath
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | | | - Rainald Moessner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Jubel Morgan
- University of Utah, Salt Lake City, Utah, United States of America
| | - Heike Muller
- University College London, London, United Kingdom
| | - Dennis L. Murphy
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda, Maryland, United States of America
| | - Allan L. Naarden
- Department of Clinical Research, Medical City Dallas Hospital, Dallas, Texas, United States of America
| | | | - Roel A. Ophoff
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center, Utrecht, The Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Andrew J. Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Michele T. Pato
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Carlos N. Pato
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John Piacentini
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - Christopher Pittenger
- Departments of Psychiatry and Psychology and the Child Study Center, Yale University, New Haven, Connecticut, United States of America
| | - Yehuda Pollak
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Scott L. Rauch
- Partners Psychiatry and McLean Hospital, Boston, Massachusetts, United States of America
| | - Tobias J. Renner
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Victor I. Reus
- Department of Psychiatry, University of California at San Francisco, San Francisco, California, United States of America
| | - Margaret A. Richter
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Frederick W. Thompson Anxiety Disorders Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Mark A. Riddle
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mary M. Robertson
- University College London, London, United Kingdom
- St George's Hospital and Medical School, London, United Kingdom
| | | | - Maria C. Rosàrio
- Child and Adolescent Psychiatry Unit (UPIA), Department of Psychiatry, Federal University of São Paulo, São Paulo, Brazil
| | - David Rosenberg
- Department of Psychiatry & Behavioral Neurosciences, Wayne State University and the Detroit Medical Center, Detroit, Michigan, United States of America
| | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Stephan Ruhrmann
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | | | - Aline S. Sampaio
- Department of Psychiatry, Faculdade de Medicina da Universidade de Säo Paulo, Brazil
- University Health Care Services - SMURB, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Jack Samuels
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Paul Sandor
- Department of Psychiatry, University of Toronto and University Health Network, Toronto Western Research Institute and Youthdale Treatment Centers, Toronto, Ontario, Canada
| | - Brooke Sheppard
- Department of Psychiatry, University of California at San Francisco, San Francisco, California, United States of America
| | - Harvey S. Singer
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jan H. Smit
- Department of Psychiatry, VU University Medical Center, Amsterdam, The Netherlands
| | - Dan J. Stein
- University of Cape Town, Cape Town, South Africa
| | - E. Strengman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jay A. Tischfield
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, United States of America
| | | | - Homero Vallada
- Department of Psychiatry, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Jeremy Veenstra-VanderWeele
- Departments of Psychiatry, Pediatrics, and Pharmacology, Kennedy Center for Research on Human Development, and Brain Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry, University of Zurich, Zurich, Switzerland
- Department of Child and Adolescent Psychiatry, University of Würzburg, Würzburg, Germany
| | - Ying Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jens R. Wendland
- Laboratory of Clinical Science, NIMH Intramural Research Program, Bethesda, Maryland, United States of America
| | - Herman G. M. Westenberg
- Department of Psychiatry, Academic Medical Center and Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Yin Yao Shugart
- Unit on Statistical Genomics, NIMH Intramural Research Program, Bethesda, Maryland, United States of America
| | - Euripedes C. Miguel
- Department of Psychiatry, University of São Paulo Medical School, São Paulo, Brazil
| | - William McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael Wagner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Humberto Nicolini
- National Institute of Genomic Medicine-SAP, Carracci Medical Group, Mexico City, Mexico
| | - Danielle Posthuma
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, De Boelelaan, Amsterdam, The Netherlands
- Department of Clinical Genetics, VU Medical Centre, De Boelelaan, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Gregory L. Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter Heutink
- Section of Medical Genomics, Department of Clinical Genetics, VU University Medical Center Amsterdam, The Netherlands
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Damiaan Denys
- Department of Psychiatry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Paul D. Arnold
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - David L. Pauls
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Naomi R. Wray
- The University of Queensland, Queensland Brain Institute, Queensland, Australia
| | - S. Evelyn Stewart
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- British Columbia Mental Health and Addictions Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carol A. Mathews
- Department of Psychiatry, University of California at San Francisco, San Francisco, California, United States of America
| | - James A. Knowles
- Department of Psychiatry and the Behavioral Sciences, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Nancy J. Cox
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Jeremiah M. Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Division of Cognitive and Behavioral Neurology, Brigham and Womens Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (LKD); (JMS)
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Bentley MJ, Lin H, Fernandez TV, Lee M, Yrigollen CM, Pakstis AJ, Katsovich L, Olds DL, Grigorenko EL, Leckman JF. Gene variants associated with antisocial behaviour: a latent variable approach. J Child Psychol Psychiatry 2013; 54:1074-85. [PMID: 23822756 PMCID: PMC3766409 DOI: 10.1111/jcpp.12109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2013] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The aim of this study was to determine if a latent variable approach might be useful in identifying shared variance across genetic risk alleles that is associated with antisocial behaviour at age 15 years. METHODS Using a conventional latent variable approach, we derived an antisocial phenotype in 328 adolescents utilizing data from a 15-year follow-up of a randomized trial of a prenatal and infancy nurse-home visitation programme in Elmira, New York. We then investigated, via a novel latent variable approach, 450 informative genetic polymorphisms in 71 genes previously associated with antisocial behaviour, drug use, affiliative behaviours and stress response in 241 consenting individuals for whom DNA was available. Haplotype and Pathway analyses were also performed. RESULTS Eight single-nucleotide polymorphisms (SNPs) from eight genes contributed to the latent genetic variable that in turn accounted for 16.0% of the variance within the latent antisocial phenotype. The number of risk alleles was linearly related to the latent antisocial variable scores. Haplotypes that included the putative risk alleles for all eight genes were also associated with higher latent antisocial variable scores. In addition, 33 SNPs from 63 of the remaining genes were also significant when added to the final model. Many of these genes interact on a molecular level, forming molecular networks. The results support a role for genes related to dopamine, norepinephrine, serotonin, glutamate, opioid and cholinergic signalling as well as stress response pathways in mediating susceptibility to antisocial behaviour. CONCLUSIONS This preliminary study supports use of relevant behavioural indicators and latent variable approaches to study the potential 'co-action' of gene variants associated with antisocial behaviour. It also underscores the cumulative relevance of common genetic variants for understanding the aetiology of complex behaviour. If replicated in future studies, this approach may allow the identification of a 'shared' variance across genetic risk alleles associated with complex neuropsychiatric dimensional phenotypes using relatively small numbers of well-characterized research participants.
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Affiliation(s)
- Mary Jane Bentley
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut
| | - Haiqun Lin
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut,Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut
| | - Thomas V. Fernandez
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut
| | - Maria Lee
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut
| | - Carolyn M. Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, Davis
| | - Andrew J. Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Liliya Katsovich
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut
| | - David L. Olds
- Department of Pediatrics, School of Medicine, University of Colorado Denver, Colorado
| | - Elena L. Grigorenko
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut,Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut
| | - James F. Leckman
- Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut
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Heffelfinger C, Pakstis AJ, Speed WC, Clark AP, Haigh E, Fang R, Furtado MR, Kidd KK, Snyder MP. Haplotype structure and positive selection at TLR1. Eur J Hum Genet 2013; 22:551-7. [PMID: 24002163 DOI: 10.1038/ejhg.2013.194] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 07/02/2013] [Accepted: 07/24/2013] [Indexed: 11/09/2022] Open
Abstract
Toll-like receptor 1, when dimerized with Toll-like receptor 2, is a cell surface receptor that, upon recognition of bacterial lipoproteins, activates the innate immune system. Variants in TLR1 associate with the risk of a variety of medical conditions and diseases, including sepsis, leprosy, tuberculosis, and others. The foremost of these is rs5743618 c.2079T>G(p.(Ile602Ser)), the derived allele of which is associated with reduced risk of sepsis, leprosy, and other diseases. Interestingly, 602Ser, which shows signatures of selection, inhibits TLR1 surface trafficking and subsequent activation of NFκB upon recognition of a ligand. This suggests that reduced TLR1 activity may be beneficial for human health. To better understand TLR1 variation and its link to human health, we have typed all 7 high-frequency missense variants (>5% in at least one population) along with 17 other variants in and around TLR1 in 2548 individuals from 56 populations from around the globe. We have also found additional signatures of selection on missense variants not associated with rs5743618, suggesting that there may be multiple functional alleles under positive selection in this gene.
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Affiliation(s)
- Christopher Heffelfinger
- 1] Department of Genetics, Yale University, New Haven, CT, USA [2] Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | | | | | - Eva Haigh
- Department of Genetics, Yale University, New Haven, CT, USA
| | | | - Mahohar R Furtado
- 1] Life Technologies, Foster City, CA, USA [2] President & Founder, Biology for Global Good, Sam Ramon, CA, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University, New Haven, CT, USA
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Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb. Investig Genet 2012; 3:18. [PMID: 22938150 PMCID: PMC3488007 DOI: 10.1186/2041-2223-3-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 06/22/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited. METHODS The back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts. RESULTS We present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color. CONCLUSION The current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O.Box 208005, New Haven, CT 06520-8005, USA
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Santoro N, Zhang CK, Zhao H, Pakstis AJ, Kim G, Kursawe R, Dykas DJ, Bale AE, Giannini C, Pierpont B, Shaw MM, Leif G, Caprio S. Variant in the glucokinase regulatory protein (GCKR) gene is associated with fatty liver in obese children and adolescents. Hepatology 2012; 55:781-9. [PMID: 22105854 PMCID: PMC3288435 DOI: 10.1002/hep.24806] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/07/2011] [Indexed: 12/11/2022]
Abstract
UNLABELLED Recently, the single nucleotide polymorphism (SNP) identified as rs1260326, in the glucokinase regulatory protein (GCKR), was associated with hypertriglyceridemia in adults. Because accumulation of triglycerides in hepatocytes represents the hallmark of steatosis, we aimed to investigate whether this variant might be associated with fatty liver (hepatic fat content, HFF%). Moreover, because recently rs738409 in the PNPLA3 and rs2854116 in the APOC3 were associated with fatty liver, we explored how the GCKR SNP and these two variants jointly influence hepatosteatosis. We studied 455 obese children and adolescents (181 Caucasians, 139 African Americans, and 135 Hispanics). All underwent an oral glucose tolerance test and fasting lipoprotein subclasses measurement by proton nuclear magnetic resonance. A subset of 142 children underwent a fast gradient magnetic resonance imaging to measure the HFF%. The rs1260326 was associated with elevated triglycerides (Caucasians P = 0.00014; African Americans P = 0.00417), large very low-density lipoprotein (VLDL) (Caucasians P = 0.001; African Americans, P = 0.03), and with fatty liver (Caucasians P = 0.034; African Americans P = 0.00002; and Hispanics P = 0.016). The PNPLA3, but not the APOC3 rs2854116 SNP, was associated with fatty liver but not with triglyceride levels. There was a joint effect between the PNPLA3 and GCKR SNPs, explaining 32% of HFF% variance in Caucasians (P = 0.00161), 39.0% in African Americans (P = 0.00000496), and 15% in Hispanics (P = 0.00342). CONCLUSION The rs1260326 in GCKR is associated with hepatic fat accumulation along with large VLDL and triglyceride levels. GCKR and PNPLA3 act together to convey susceptibility to fatty liver in obese youths.
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Affiliation(s)
- Nicola Santoro
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Clarence K. Zhang
- Yale Center for Statistical Genomics and Proteomics, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Hongyu Zhao
- Yale Center for Statistical Genomics and Proteomics, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Grace Kim
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Romy Kursawe
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Daniel J. Dykas
- Department of Genetics, Yale University School of Medicine, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Allen E. Bale
- Department of Genetics, Yale University School of Medicine, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Cosimo Giannini
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Bridget Pierpont
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Melissa M. Shaw
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Groop Leif
- Department of Clinical Sciences/Diabetes & Endocrinology and Lund University Diabetes Centre, Lund University, University Hospital, Malmoe, Malmoe, Sweden
| | - Sonia Caprio
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT
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Abstract
ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics and Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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Kidd JR, Friedlaender F, Pakstis AJ, Furtado M, Fang R, Wang X, Nievergelt CM, Kidd KK. Single nucleotide polymorphisms and haplotypes in Native American populations. Am J Phys Anthropol 2011; 146:495-502. [PMID: 21913176 DOI: 10.1002/ajpa.21560] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 04/26/2011] [Indexed: 11/06/2022]
Abstract
Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. At the same time that autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history. In the current study, we are using data on nine Native American populations to compare the results based on a large haplotype-based dataset with relatively small independent sets of single nucleotide polymorphisms. We are interested in what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can we differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can we infer the historical/evolutionary relationships among Native American populations and their Eurasian origins? We conclude that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using our largest dataset, we see a general increasing distance from Old World populations from North to South in the New World except for an unexplained close relationship between our Maya and Quechua samples.
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Affiliation(s)
- Judith R Kidd
- Department of Genetics, Yale University Medical School, New Haven, CT 06520, USA.
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Abstract
A variant allele, ADH1B*48His, also known as ADH1B*2, at the human Alcohol Dehydrogenase 1B gene (ADH1B) is strongly associated with alcoholism in some populations and has an unusual geographic distribution. Strong evidence implies selection has increased the frequency of this allele in some East Asian populations but does not fully explain its geographic pattern. We have studied haplotypes of 10 single nucleotide polymorphisms (SNPs) and two short tandem repeat polymorphisms (STRPs) in the ADH1B region in 2,206 individuals from a worldwide set of populations. These SNPs and STRPs define nine common haplogroups most of which have distinct geographic patterns. The haplogroups H5 and H6, both with the derived ADH1B*48His allele, appear restricted to the Middle East and East Asia, respectively. The positively selected H7 is derived from H6 by a new regulatory region variant defining SNP rs3811801 restricted to East Asia. Age estimates of the haplogroups based on the STRPs also agree with the time of the migration events estimated by other studies. H7 is estimated to have expanded recently, around 2,800 years ago, and ancient DNA samples from North China confirm its presence about that time. The dating of the H7 expansion may help understand the selective force on the ADH1B gene.
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Affiliation(s)
- Hui Li
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Sheng Gu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Yi Han
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Zhi Xu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Andrew J. Pakstis
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Judith R. Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
| | - Kenneth K. Kidd
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520 USA
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Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK. Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples. Investig Genet 2011; 2:1. [PMID: 21208434 PMCID: PMC3025953 DOI: 10.1186/2041-2223-2-1] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 01/05/2011] [Indexed: 12/02/2022]
Abstract
Background Using DNA to determine an individual's ancestry from among human populations is generally interesting and useful for many purposes, including admixture mapping, controlling for population structure in disease or trait association studies and forensic ancestry inference. However, to estimate ancestry, including possible admixture within an individual, as well as heterogeneity within a group of individuals, allele frequencies are necessary for what are believed to be the contributing populations. For this purpose, panels of ancestry informative markers (AIMs) have been developed. Results We are presenting our work on one such panel, composed of 128 ancestry informative single-nucleotide polymorphisms (AISNPs) already proposed in the literature. Compared to previous studies of these AISNPs, we have studied three times the number of individuals (4,871) in three times as many population samples (119). We have validated this panel for many ancestry assignment and admixture studies, especially those that were the rationale for the original selection of the 128 SNPs: African Americans and Mexican Americans. At the same time, the limitations of the panel for distinguishing ancestry and quantifying admixture among Eurasian populations are noted. Conclusion We demonstrate the simultaneous importance of the specific set of population samples and their relative sample sizes in the use of the structure program to determine which groups cluster together and consequently influence the ability of a marker panel to infer ancestry. We demonstrate the strengths and weaknesses of this particular panel of AISNPs in a global context.
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Affiliation(s)
- Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
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Grigorenko EL, De Young CG, Eastman M, Getchell M, Haeffel GJ, Klinteberg BA, Koposov RA, Oreland L, Pakstis AJ, Ponomarev OA, Ruchkin VV, Singh JP, Yrigollen CM. Aggressive behavior, related conduct problems, and variation in genes affecting dopamine turnover. Aggress Behav 2010; 36:158-76. [PMID: 20127808 DOI: 10.1002/ab.20339] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A number of dopamine-related genes have been implicated in the etiology of violent behavior and conduct problems. Of these genes, the ones that code for the enzymes that influence the turnover of dopamine (DA) have received the most attention. In this study, we investigated 12 genetic polymorphisms in four genes involved with DA functioning (COMT, MAOA and MAOB, and DbetaH) in 179 incarcerated male Russian adolescents and two groups of matched controls: boys without criminal records referred to by their teachers as (a) "troubled-behavior-free" boys, n=182; and (b) "troubled-behavior" boys, n=60. The participants were classified as (1) being incarcerated or not, (2) having the DSM-IV diagnosis of conduct disorder (CD) or not, and (3) having committed violent or nonviolent crimes (for the incarcerated individuals only). The findings indicate that, although no single genetic variant in any of the four genes differentiated individuals in the investigated groups, various linear combinations (i.e., haplotypes) and nonlinear combinations (i.e., interactions between variants within and across genes) of genetic variants resulted in informative and robust classifications for two of the three groupings. These combinations of genetic variants differentiated individuals in incarceration vs. nonincarcerated and CD vs. no-CD groups; no informative combinations were established consistently for the grouping by crime within the incarcerated individuals. This study underscores the importance of considering multiple rather than single markers within candidate genes and their additive and interactive combinations, both with themselves and with nongenetic indicators, while attempting to understand the genetic background of such complex behaviors as serious conduct problems.
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Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, Kidd KK. SNPs for a universal individual identification panel. Hum Genet 2010; 127:315-24. [PMID: 19937056 DOI: 10.1007/s00439-009-0771-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 11/13/2009] [Indexed: 10/20/2022]
Abstract
An efficient method to uniquely identify every individual would have value in quality control and sample tracking of large collections of cell lines or DNA as is now often the case with whole genome association studies. Such a method would also be useful in forensics. SNPs represent the best markers for such purposes. We have developed a globally applicable resource of 92 SNPs for individual identification (IISNPs) with extremely low probabilities of any two unrelated individuals from anywhere in the world having identical genotypes. The SNPs were identified by screening over 500 likely/candidate SNPs on samples of 44 populations representing the major regions of the world. All 92 IISNPs have an average heterozygosity [0.4 and the F(st) values are all\0.06 on our 44 populations making these a universally applicable panel irrespective of ethnicity or ancestry. No significant linkage disequilibrium (LD) occurs for all unique pairings of 86 of the 92 IISNPs (median LD = 0.011) in all of the 44 populations. The remaining 6 IISNPs show strong LD in most of the 44 populations for a small subset (7) of the unique pairings in which they occur due to close linkage. 45 of the 86 SNPs are spread across the 22 human autosomes and show very loose or no genetic linkage with each other. These 45 IISNPs constitute an excellent panel for individual identification including paternity testing with associated probabilities of individual genotypes less than 10(-15), smaller than achieved with the current panels of forensic markers. This panel also improves on an interim panel of 40 IISNPs previously identified using 40 population samples. The unlinked status of the subset of 45 SNPs we have identified also makes them useful for situations involving close biological relationships. Comparisons with random sets of SNPs illustrate the greater discriminating power, efficiency, and more universal applicability of this IISNP panel to populations around the world. The full set of 86 IISNPs that do not show LD can be used to provide even smaller genotype match probabilities in the range of 10(-31)-10(-35) based on the 44 population samples studied.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, 208005, New Haven, CT 06520, USA
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Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Mehdi SQ, Kajuna SLB, Barta C, Kungulilo S, Karoma NJ, Lu RB, Zhukova OV, Kim JJ, Comas D, Siniscalco M, New M, Li P, Li H, Manolopoulos VG, Speed WC, Rajeevan H, Pakstis AJ, Kidd JR, Kidd KK. The distribution and most recent common ancestor of the 17q21 inversion in humans. Am J Hum Genet 2010; 86:161-71. [PMID: 20116045 DOI: 10.1016/j.ajhg.2010.01.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/17/2009] [Accepted: 01/05/2010] [Indexed: 11/17/2022] Open
Abstract
The polymorphic inversion on 17q21, sometimes called the microtubular associated protein tau (MAPT) inversion, is an approximately 900 kb inversion found primarily in Europeans and Southwest Asians. We have identified 21 SNPs that act as markers of the inverted, i.e., H2, haplotype. The inversion is found at the highest frequencies in Southwest Asia and Southern Europe (frequencies of approximately 30%); elsewhere in Europe, frequencies vary from < 5%, in Finns, to 28%, in Orcadians. The H2 inversion haplotype also occurs at low frequencies in Africa, Central Asia, East Asia, and the Americas, though the East Asian and Amerindian alleles may be due to recent gene flow from Europe. Molecular evolution analyses indicate that the H2 haplotype originally arose in Africa or Southwest Asia. Though the H2 inversion has many fixed differences across the approximately 900 kb, short tandem repeat polymorphism data indicate a very recent date for the most recent common ancestor, with dates ranging from 13,600 to 108,400 years, depending on assumptions and estimation methods. This estimate range is much more recent than the 3 million year age estimated by Stefansson et al. in 2005.
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Affiliation(s)
- Michael P Donnelly
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06520, USA
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Mukherjee N, Kidd KK, Pakstis AJ, Speed WC, Li H, Tarnok Z, Barta C, Kajuna SLB, Kidd JR. The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Mol Psychiatry 2010; 15:216-25. [PMID: 18574484 PMCID: PMC2811226 DOI: 10.1038/mp.2008.64] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic variation at the catechol-O-methyltransferase (COMT) gene has been significantly associated with risk for various neuropsychiatric conditions such as schizophrenia, panic disorder, bipolar disorders, anorexia nervosa and others. It has also been associated with nicotine dependence, sensitivity to pain and cognitive dysfunctions especially in schizophrenia. The non-synonymous single nucleotide polymorphism (SNP) in exon 4--Val108/158Met--is the most studied SNP at COMT and is the basis for most associations. It is not, however, the only variation in the gene; several haplotypes exist across the gene. Some studies indicate that the haplotypic combinations of alleles at the Val108/158Met SNP with those in the promoter region and in the 3'-untranslated region are responsible for the associations with disorders and not the non-synonymous SNP by itself. We have now studied DNA samples from 45 populations for 63 SNPs in a region of 172 kb across the region of 22q11.2 encompassing the COMT gene. We focused on 28 SNPs spanning the COMT-coding region and immediately flanking DNA, and found that the haplotypes are from diverse evolutionary lineages that could harbor as yet undetected variants with functional consequences. Future association studies should be based on SNPs that define the common haplotypes in the population(s) being studied.
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Affiliation(s)
- N Mukherjee
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - KK Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - AJ Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - WC Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - H Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511
| | - Z Tarnok
- Vadaskert Child and Adolescent Psychiatric clinic, Budapest, Hungary
| | - C Barta
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest,Hungary
| | - SLB Kajuna
- Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - JR Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA - 06511,Correspondence to: Judith Kidd. Ph.D Department of Genetics, Yale University School of Medicine, P.O. Box 208005, 333 Cedar Street, New Haven, CT-06520-8005. E-mail:
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Fang R, Pakstis AJ, Hyland F, Wang D, Shewale J, Kidd JR, Kidd KK, Furtado MR. Multiplexed SNP detection panels for human identification. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.08.161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Luo HR, Wu GS, Pakstis AJ, Tong L, Oota H, Kidd KK, Zhang YP. Origin and dispersal of atypical aldehyde dehydrogenase ALDH2487Lys. Gene 2009; 435:96-103. [PMID: 19393179 DOI: 10.1016/j.gene.2008.12.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/24/2008] [Indexed: 10/21/2022]
Abstract
The East Asian respond with a marked facial flushing and mild to moderate symptoms of intoxication after drinking the amounts of alcohol that has no detectable effect on European. The alcohol sensitivity in Orientals is due to a delayed oxidation of acetaldehyde by an atypical aldehyde dehydrogenase ALDH2487Lys, which is resulted from a structural mutation in gene ALDH2. The atypical ALDH2487Lys allele has been associated with various phenotypic statuses, such as protective against alcohol dependence and the risk of alcohol-related digestive tract cancers. Here, we have examined this SNP, adjacent four non-coding SNPs, and one downstream STRP on ALDH2 gene, in total of 1072 unrelated healthy individuals from 14 Chinese populations and 130 Indian individuals. Five major haplotypes based on five SNPs across the ALDH2 gene 40 kb were found in all East Asian populations. The frequencies of the ancestral haplotype GCCTG and the East Asian special haplotype GCCTA containing the atypical ALDH2487Lys allele were 44.8% and 14.9%, respectively. The frequency of the atypical ALDH2487Lys allele or the East Asian specific haplotype GCCTA is high in Yunnan, South coastal, east coastal of China, and decreased gradually toward inland China, West, Northwest and North China. Combined with demographic history in East Asian, our results showed that the presence of ALDH2487Lys allele in peripheral regions of China might be the results of historical migration events from China to these regions. The origin of ALDH2487Lys could be possibly traced back to ancient Pai-Yuei tribe in South China.
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Affiliation(s)
- Huai-Rong Luo
- Kunming Institute of Zoology, The Chinese Academy of Sciences, Yunnan, China
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Speed WC, O'Roak BJ, Tárnok Z, Barta C, Pakstis AJ, State MW, Kidd KK. Haplotype evolution of SLITRK1, a candidate gene for Gilles de la Tourette syndrome. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:463-6. [PMID: 18004766 DOI: 10.1002/ajmg.b.30641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gilles de la Tourette syndrome (GTS) is a complex disorder with a clear genetic component but no clearly identified genes with variation of etiologic relevance. Various candidate regions and genes show some evidence of affecting risk, though clearly not all patients/families can be explained by any one of them. Resequencing one candidate gene, SLITRK1, has identified four new variants. Including them, we have typed over 2,300 normal individuals from 44 populations for 11 SNPs spanning the gene. The unusual global pattern seen is that one non-ancestral haplotype is the single most common haplotype worldwide. Other haplotypes appear to result from accumulation of mutations with no evidence of historical recombination. Although there is no evidence of selection, the haplotype frequency variation seen around the world will need to be considered in any future association studies of this locus with GTS or any other neuropsychiatric disorder.
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Affiliation(s)
- William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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Li H, Gu S, Cai X, Speed WC, Pakstis AJ, Golub EI, Kidd JR, Kidd KK. Ethnic related selection for an ADH Class I variant within East Asia. PLoS One 2008; 3:e1881. [PMID: 18382665 PMCID: PMC2268739 DOI: 10.1371/journal.pone.0001881] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 02/25/2008] [Indexed: 11/18/2022] Open
Abstract
Background The alcohol dehydrogenases (ADH) are widely studied enzymes and the evolution of the mammalian gene cluster encoding these enzymes is also well studied. Previous studies have shown that the ADH1B*47His allele at one of the seven genes in humans is associated with a decrease in the risk of alcoholism and the core molecular region with this allele has been selected for in some East Asian populations. As the frequency of ADH1B*47His is highest in East Asia, and very low in most of the rest of the world, we have undertaken more detailed investigation in this geographic region. Methodology/Principal Findings Here we report new data on 30 SNPs in the ADH7 and Class I ADH region in samples of 24 populations from China and Laos. These populations cover a wide geographic region and diverse ethnicities. Combined with our previously published East Asian data for these SNPs in 8 populations, we have typed populations from all of the 6 major linguistic phyla (Altaic including Korean-Japanese and inland Altaic, Sino-Tibetan, Hmong-Mien, Austro-Asiatic, Daic, and Austronesian). The ADH1B genotyping data are strongly related to ethnicity. Only some eastern ethnic phyla or subphyla (Korean-Japanese, Han Chinese, Hmong-Mien, Daic, and Austronesian) have a high frequency of ADH1B*47His. ADH1B haplotype data clustered the populations into linguistic subphyla, and divided the subphyla into eastern and western parts. In the Hmong-Mien and Altaic populations, the extended haplotype homozygosity (EHH) and relative EHH (REHH) tests for the ADH1B core were consistent with selection for the haplotype with derived SNP alleles. In the other ethnic phyla, the core showed only a weak signal of selection at best. Conclusions/Significance The selection distribution is more significantly correlated with the frequency of the derived ADH1B regulatory region polymorphism than the derived amino-acid altering allele ADH1B*47His. Thus, the real focus of selection may be the regulatory region. The obvious ethnicity-related distributions of ADH1B diversities suggest the existence of some culture-related selective forces that have acted on the ADH1B region.
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Affiliation(s)
- Hui Li
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
- MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Sheng Gu
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Xiaoyun Cai
- MOE Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - William C. Speed
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Andrew J. Pakstis
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Efim I. Golub
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Judith R. Kidd
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Kenneth K. Kidd
- Lab for Human Polymorphism Studies, Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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42
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Han Y, Gu S, Oota H, Osier MV, Pakstis AJ, Speed WC, Kidd JR, Kidd KK. Evidence of positive selection on a class I ADH locus. Am J Hum Genet 2007; 80:441-56. [PMID: 17273965 PMCID: PMC1821113 DOI: 10.1086/512485] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 01/05/2007] [Indexed: 11/03/2022] Open
Abstract
The alcohol dehydrogenase (ADH) family of enzymes catalyzes the reversible oxidation of alcohol to acetaldehyde. Seven ADH genes exist in a segment of ~370 kb on 4q21. Products of the three class I ADH genes that share 95% sequence identity are believed to play the major role in the first step of ethanol metabolism. Because the common belief that selection has operated at the ADH1B*47His allele in East Asian populations lacks direct biological or statistical evidence, we used genomic data to test the hypothesis. Data consisted of 54 single-nucleotide polymorphisms (SNPs) across the ADH clusters in a global sampling of 42 populations. Both the F(st) statistic and the long-range haplotype (LRH) test provided positive evidence of selection in several East Asian populations. The ADH1B Arg47His functional polymorphism has the highest F(st) of the 54 SNPs in the ADH cluster, and it is significantly above the mean F(st) of 382 presumably neutral sites tested on the same 42 population samples. The LRH test that uses cores including that site and extending on both sides also gives significant evidence of positive selection in some East Asian populations for a specific haplotype carrying the ADH1B*47His allele. Interestingly, this haplotype is present at a high frequency in only some East Asian populations, whereas the specific allele also exists in other East Asian populations and in the Near East and Europe but does not show evidence of selection with use of the LRH test. Although the ADH1B*47His allele conveys a well-confirmed protection against alcoholism, that modern phenotypic manifestation does not easily translate into a positive selective force, and the nature of that selective force, in the past and/or currently, remains speculative.
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Affiliation(s)
- Yi Han
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA
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43
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Abstract
Single nucleotide polymorphisms (SNPs) are likely in the near future to have a fundamental role both in human identification and description. However, because allele frequencies can vary greatly among populations, a critical issue is the population genetics underlying calculation of the probabilities of unrelated individuals having identical multi-locus genotypes. Here we report on progress in identifying SNPs that show little allele frequency variation among a worldwide sample of 40 populations, i.e., have a low F(st), while remaining highly informative. Such markers have match probabilities that are nearly uniform irrespective of population and become candidates for a universally applicable individual identification panel applicable in forensics and paternity testing. They are also immediately useful for efficient sample identification/tagging in large biomedical, association, and epidemiologic studies. Using our previously described strategy for both identifying and characterizing such SNPs (Kidd et al. in Forensic Sci Int 164:20-32, 2006), we have now screened a total of 432 SNPs likely a priori to have high heterozygosity and low allele frequency variation and from these have selected the markers with the lowest F(st) in our set of 40 populations to produce a panel of 40 low F(st), high heterozygosity SNPs. Collectively these SNPs give average match probabilities of less than 10(-16) in most of the 40 populations and less than 10(-14) in all but one small isolated population; the range is 2.02 x 10(-17) to 1.29 x 10(-13). These 40 SNPs constitute excellent candidates for the global forensic community to consider for a universally applicable SNP panel for human identification. The relative ease with which these markers could be identified also provides a cautionary lesson for investigations of possible balancing selection.
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Affiliation(s)
- Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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Rajeevan H, Cheung KH, Gadagkar R, Stein S, Soundararajan U, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: an allele frequency database for microevolutionary studies. Evol Bioinform Online 2007; 1:1-10. [PMID: 19325849 PMCID: PMC2658869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
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Affiliation(s)
- Haseena Rajeevan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kei-Hoi Cheung
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA, Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Rohit Gadagkar
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Shannon Stein
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Usha Soundararajan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Perry L Miller
- Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA,Correspondence: Kenneth K. Kidd, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005, USA, Telephone: 203-785-2654, Fax: 203-785-6568,
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Gu S, Pakstis AJ, Li H, Speed WC, Kidd JR, Kidd KK. Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations. Eur J Hum Genet 2007; 15:302-12. [PMID: 17202997 DOI: 10.1038/sj.ejhg.5201751] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The initial belief that haplotype block boundaries and haplotypes were largely shared across populations was a foundation for constructing a haplotype map of the human genome using common SNP markers. The HapMap data document the generality of a block-like pattern of linkage disequilibrium (LD) with regions of low and high haplotype diversity but differences among the populations. Studies of many additional populations demonstrate that LD patterns can be highly variable among populations both across and within geographic regions. Because of this variation, emphasis has shifted to the generalizability of tagSNPs, those SNPs that capture the bulk of variation in a region. We have examined the LD and tagSNP patterns based upon over 2000 individual samples in 38 populations and 134 SNPs in 10 genetically independent loci for a total of 517 kb with an average density of 1 SNP/5 kb. Four different 'block' definitions and the pairwise LD tagSNP selection algorithm have been applied. Our results not only confirm large variation in block partition among populations from different regions (agreeing with previous studies including the HapMap) but also show that significant variation can occur among populations within geographic regions. None of the block-defining algorithms produces a consistent pattern within or across all geographic groups. In contrast, tagSNP transferability is much greater than the similarity of LD patterns and, although not perfect, some generalizations of transferability are possible. The analyses show an asymmetric pattern of tagSNP transferability coinciding with the subsetting of variation attributed to the spread of modern humans around the world.
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Affiliation(s)
- Sheng Gu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
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Abstract
The optimal method to be used for tSNP selection, the applicability of a reference LD map to unassayed populations, and the scalability of these methods to genome-wide analysis, all remain subjects of debate. We propose novel, scalable matrix algorithms that address these issues and we evaluate them on genotypic data from 38 populations and four genomic regions (248 SNPs typed for approximately 2000 individuals). We also evaluate these algorithms on a second data set consisting of genotypes available from the HapMap database (1336 SNPs for four populations) over the same genomic regions. Furthermore, we test these methods in the setting of a real association study using a publicly available family data set. The algorithms we use for tSNP selection and unassayed SNP reconstruction do not require haplotype inference and they are, in principle, scalable even to genome-wide analysis. Moreover, they are greedy variants of recently developed matrix algorithms with provable performance guarantees. Using a small set of carefully selected tSNPs, we achieve very good reconstruction accuracy of "untyped" genotypes for most of the populations studied. Additionally, we demonstrate in a quantitative manner that the chosen tSNPs exhibit substantial transferability, both within and across different geographic regions. Finally, we show that reconstruction can be applied to retrieve significant SNP associations with disease, with important genotyping savings.
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Affiliation(s)
- Peristera Paschou
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA.
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47
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Oota H, Dunn CW, Speed WC, Pakstis AJ, Palmatier MA, Kidd JR, Kidd KK. Conservative evolution in duplicated genes of the primate Class I ADH cluster. Gene 2006; 392:64-76. [PMID: 17204375 DOI: 10.1016/j.gene.2006.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Revised: 11/11/2006] [Accepted: 11/15/2006] [Indexed: 11/22/2022]
Abstract
Humans have seven alcohol dehydrogenase genes (ADH) falling into five classes. Three out of the seven genes (ADH1A, ADH1B and ADH1C) belonging to Class I are expressed primarily in liver and code the main enzymes catalyzing ethanol oxidization. The three genes are tandemly arrayed within the ADH cluster on chromosome 4 and have very high nucleotide similarity to each other (exons: >90%; introns: >70%), suggesting the genes have been generated by duplication event(s). One explanation for maintaining similarity of such clustered genes is homogenization via gene conversion(s). Alternatively, recency of the duplications or some other functional constraints might explain the high similarities among the genes. To test for gene conversion, we sequenced introns 2, 3, and 8 of all three Class I genes (total>15.0 kb) for five non-human primates--four great apes and one Old World Monkey (OWM)--and compared them with those of humans. The phylogenetic analysis shows each intron sequence clusters strongly within each gene, giving no evidence for gene conversion(s). Several lines of evidence indicate that the first split was between ADH1C and the gene that gave rise to ADH1A and ADH1B. We also analyzed cDNA sequences of the three genes that have been previously reported in mouse and Catarrhines (OWMs, chimpanzee, and humans) and found that the synonymous and non-synonymous substitution (dN/dS) ratios in all pairs are less than 1 representing purifying selection. This suggests that purifying selection is more important than gene conversion(s) in maintaining the overall sequence similarity among the Class I genes. We speculate that the highly conserved sequences on the three duplicated genes in primates have been achieved essentially by maintaining stability of the hetero-dimer formation that might have been related to dietary adaptation in primate evolution.
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Affiliation(s)
- Hiroki Oota
- Department of Genetics, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520-8005, USA.
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Han Y, Oota H, Osier MV, Pakstis AJ, Speed WC, Odunsi A, Okonofua F, Kajuna SLB, Karoma NJ, Kungulilo S, Grigorenko E, Zhukova OV, Bonne-Tamir B, Lu RB, Parnas J, Schulz LO, Kidd JR, Kidd KK. Considerable haplotype diversity within the 23kb encompassing the ADH7 gene. Alcohol Clin Exp Res 2006; 29:2091-100. [PMID: 16385178 DOI: 10.1097/01.alc.0000191769.92667.04] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Of the seven known human alcohol dehydrogenase (ADH) genes, the non-liver expressed ADH7 gene codes for the enzyme with the highest maximal activity for ethanol. Previous study from our laboratory has suggested that ADH7 has an epistatic role for protection against alcoholism based on a single ADH7 SNP. METHODS We have now studied seven SNPs, additional populations for the SNP previously examined, and six more new SNPs, across 23 kb of ADH7 in 38 population samples originating from different geographical regions of the world. RESULTS The overall linkage disequilibrium is moderate to strong across this region even though considerable 7-SNP haplotype diversity is observed. This uncommonly high haplotype diversity is explained by high LD within each "half," the three upstream SNPs and the four downstream SNPs, but near randomization between the "halves." This division significantly simplified the haplotype pattern: only four major haplotypes account for almost all chromosomes in all populations in each "half." CONCLUSIONS The low linkage disequilibrium between these two "halves" suggests multiple recombination(s) have occurred in this region, specifically, within intron 7. The absence of strong LD between the functional variation in ADH1B that is strongly associated with alcoholism and any of the variation in ADH7 supports the genetic independence of ADH7 in association studies. Thus, the previously observed epistatic effect of ADH7 cannot be explained by its linkage disequilibrium with a causative factor in ADH1B.
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Affiliation(s)
- Yi Han
- Department of Genetics, Yale University, School of Medicine, New Haven, CT 06520-8005, USA
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Abstract
UNLABELLED Understanding of human variation relevant to association studies can benefit from population comparison, especially comparing populations in the same geographical region. Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern. We present here a win32 system based Perl/Tk application for visual comparisons of these variations in different populations. AVAILABILITY The application package is available at http://info.med.yale.edu/genetics/kkidd/programs.html CONTACT sheng.gu@yale.edu.
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Affiliation(s)
- Sheng Gu
- Department of Genetics, Yale University School of Medicine, New Haven, USA.
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Sawyer SL, Mukherjee N, Pakstis AJ, Feuk L, Kidd JR, Brookes AJ, Kidd KK. Linkage disequilibrium patterns vary substantially among populations. Eur J Hum Genet 2005; 13:677-86. [PMID: 15657612 DOI: 10.1038/sj.ejhg.5201368] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A major initiative to create a global human haplotype map has recently been launched as a tool to improve the efficiency of disease gene mapping. The 'HapMap' project will study common variants in depth in four (and to a lesser degree in up to 12) populations to catalogue haplotypes that are expected to be common to all populations. A hope of the 'HapMap' project is that much of the genome occurs in regions of limited diversity such that only a few of the SNPs in each region will capture the diversity and be relevant around the world. In order to explore the implications of studying only a limited number of populations, we have analyzed linkage disequilibrium (LD) patterns of three 175-320 kb genomic regions in 16 diverse populations with an emphasis on African and European populations. Analyses of these three genomic regions provide empiric demonstration of marked differences in frequencies of the same few haplotypes, resulting in differences in the amount of LD and very different sets of haplotype frequencies. These results highlight the distinction between the statistical concept of LD and the biological reality of haplotypes and their frequencies. The significant quantitative and qualitative variation in LD among populations, even for populations within a geographic region, emphasizes the importance of studying diverse populations in the HapMap project to assure broad applicability of the results.
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Affiliation(s)
- Sarah L Sawyer
- Center for Genomics and Bioinformatics, Karolinska Institute, Berzelius väg 35, Stockholm 17177, Sweden
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