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Durand K, Yainna S, Nam K. Population genomics unravels a lag phase during the global fall armyworm invasion. Commun Biol 2024; 7:957. [PMID: 39117774 PMCID: PMC11310199 DOI: 10.1038/s42003-024-06634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
The time that elapsed between the initial introduction and the proliferation of an invasive species is referred to as the lag phase. The identification of the lag phase is critical for generating plans for pest management and for the prevention of biosecurity failure. However, lag phases have been identified mostly through retrospective searches of historical records. The agricultural pest fall armyworm (FAW; Spodoptera frugiperda) is native to the New World. FAW invasion was first reported from West Africa in 2016, then it spread quickly through Africa, Asia, and Oceania. Here, using population genomics approaches, we demonstrate that the FAW invasion involved an undocumented lag phase. Invasive FAW populations have negative signs of genomic Tajima's D, and invasive population-specific genetic variations have particularly decreased Tajima's D, supporting a substantial amount of time for the generation of new mutations in introduced FAW populations. Model-based diffusion approximations support the existence of a period with a cessation of gene flow between native and invasive FAW populations. Taken together, these results provide strong support for the presence of a lag phase during the FAW invasion. These results show the usefulness of using population genomics analyses to identify lag phases in biological invasions.
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Affiliation(s)
| | | | - Kiwoong Nam
- DGIMI, INRAE, Univ Montpellier, Montpellier, France.
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2
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Pivirotto A, Peles N, Hey J. Allele age estimators designed for whole genome datasets show only a modest decrease in accuracy when applied to whole exome datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578465. [PMID: 38370640 PMCID: PMC10871225 DOI: 10.1101/2024.02.01.578465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Personalized genomics in the healthcare system is becoming increasingly accessible as the costs of sequencing decreases. With the increase in number of genomes, larger numbers of rare variants are being discovered and much work is being done to identify their functional impacts in relation to disease phenotypes. One way to characterize these variants is to estimate the time the mutation entered the population. However, allele age estimators such as Relate, Genealogical Estimator of Variant Age, and time of coalescence, were developed based on the assumption that datasets include the entire genome. We examined the performance of each of these estimators on simulated exome data under a neutral constant population size model and found that each provides usable estimates of allele age from whole-exome datasets. To test the robustness of these methods, analyses were undertaken to simulate data under a population expansion model and background selection. Relate performs the best amongst all three estimators with Pearson coefficients of 0.64 and 0.68 (neutral constant and expansion population model) with a 17 percent and 15 percent drop in accuracy between whole genome and whole exome estimations. Of the three estimators, Relate is best able to parallelize to yield quick results with little resources, however even Relate is only able to scale to thousands of samples making it unable to match the hundreds of thousands of samples being currently released. While more work is needed to expand the capabilities of current methods of estimating allele age, these methods estimate the age of mutations with a modest decrease in performance.
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Affiliation(s)
- Alyssa Pivirotto
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
| | - Noah Peles
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA USA
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3
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Vodnjov N, Toplišek J, Maver A, Čuturilo G, Jaklič H, Teran N, Višnjar T, Škrjanec Pušenjak M, Hodžić A, Miljanović O, Peterlin B, Writzl K. A novel splice-site FHOD3 founder variant is a common cause of hypertrophic cardiomyopathy in the population of the Balkans-A cohort study. PLoS One 2023; 18:e0294969. [PMID: 38051749 DOI: 10.1371/journal.pone.0294969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/11/2023] [Indexed: 12/07/2023] Open
Abstract
Founder variants in sarcomere protein genes account for a significant proportion of disease-causing variants in patients with hypertrophic cardiomyopathy (HCM). However, information on founder variants in non-sarcomeric protein genes, such as FHOD3, which have only recently been associated with HCM, remains scarce. In this study, we conducted a retrospective analysis of exome sequencing data of 134 probands with HCM for recurrent pathogenic variants. We discovered a novel likely pathogenic variant c.1646+2T>C in FHOD3 in heterozygous state in eight probands with HCM and confirmed its presence in seven additional relatives. Individuals with this variant had a wide range of ages at onset of the disease (4-63 years). No adverse cardiac events were observed. Haplotype analysis revealed that the individuals with this variant shared a genomic region of approximately 5 Mbp surrounding the variant, confirming the founder effect of the variant. FHOD3 c.1646+2T>C is estimated to have arisen 58 generations ago (95% CI: 45-81) in a common ancestor living on the Balkans. A founder FHOD3 c.1646+2T>C variant is the second most common genetic variant in our cohort of patients with HCM, occurring in 16% of probands with a known genetic cause of HCM, which represents a substantially higher proportion than the currently estimated 0.5-2% for causal FHOD3 variants. Our study broadens the understanding of the genetic causes of HCM and may improve the diagnosis of this condition, particularly in patients from the Balkans.
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Affiliation(s)
- Nina Vodnjov
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Toplišek
- Department of Cardiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Goran Čuturilo
- Department of Medical Genetics, University Children's Hospital, Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Teran
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tanja Višnjar
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Maruša Škrjanec Pušenjak
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodžić
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- European Reference Network for Rare, Low Prevalence, or Complex Diseases of the Heart (ERN GUARD-Heart)
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4
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Aretini P, Presciuttini S, Pastore A, Galli A, Panepinto S, Tancredi M, Ghilli M, Guglielmi C, Sidoti D, Congregati C, Caligo MA. The BRCA1 c.4096+1G>A Is a Founder Variant Which Originated in Ancient Times. Int J Mol Sci 2023; 24:15507. [PMID: 37958491 PMCID: PMC10648645 DOI: 10.3390/ijms242115507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Approximately 30-50% of hereditary breast and ovarian cancer (HBOC) is due to the presence of germline pathogenic variants in the BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) onco-suppressor genes, which are involved in DNA damage response. Women who carry pathogenic BRCA1 variants are particularly likely to develop breast cancer (BC) and ovarian cancer (OC), with a 45-79 percent and 39-48 percent chance, respectively. The BRCA1 c.4096+1G>A variant has been frequently ascertained in Tuscany, Italy, and it has also been detected in other Italian regions and other countries. Its pathogenetic status has been repeatedly changed from a variant of uncertain significance, to pathogenic, to likely pathogenic. In our study, 48 subjects (38 of whom are carriers) from 27 families were genotyped with the Illumina OncoArray Infinium platform (533,531 SNPs); a 20 Mb region (24.6 cM) around BRCA1, including 4130 SNPs (21 inside BRCA1) was selected for haplotype analysis. We used a phylogenetic method to estimate the time to the most recent common ancestor (MRCA) of BRCA1 c.4096+1G>A founder pathogenic variant. This analysis suggests that the MRCA lived about 155 generations ago-around 3000 years ago.
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Affiliation(s)
- Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
| | - Silvano Presciuttini
- Dipartimento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy;
| | - Aldo Pastore
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
- Laboratorio NEST, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Alvaro Galli
- Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche (CNR), 56124 Pisa, Italy;
| | - Sara Panepinto
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Mariella Tancredi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Matteo Ghilli
- Breast Unit, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Chiara Guglielmi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Diletta Sidoti
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Caterina Congregati
- Genetica Medica, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Maria Adelaide Caligo
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
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6
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Pivirotto AM, Platt A, Patel R, Kumar S, Hey J. Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561569. [PMID: 37873438 PMCID: PMC10592680 DOI: 10.1101/2023.10.09.561569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A classic population genetic prediction is that alleles experiencing directional selection should swiftly traverse allele frequency space, leaving detectable reductions in genetic variation in linked regions. However, despite this expectation, identifying clear footprints of beneficial allele passage has proven to be surprisingly challenging. We addressed the basic premise underlying this expectation by estimating the ages of large numbers of beneficial and deleterious alleles in a human population genomic data set. Deleterious alleles were found to be young, on average, given their allele frequency. However, beneficial alleles were older on average than non-coding, non-regulatory alleles of the same frequency. This finding is not consistent with directional selection and instead indicates some type of balancing selection. Among derived beneficial alleles, those fixed in the population show higher local recombination rates than those still segregating, consistent with a model in which new beneficial alleles experience an initial period of balancing selection due to linkage disequilibrium with deleterious recessive alleles. Alleles that ultimately fix following a period of balancing selection will leave a modest 'soft' sweep impact on the local variation, consistent with the overall paucity of species-wide 'hard' sweeps in human genomes.
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Affiliation(s)
| | - Alexander Platt
- Temple University, Department of Biology, Philadelphia PA 19122, USA
- University of Pennsylvania, Department of Genetics, Philadelphia PA 19104, USA
| | - Ravi Patel
- Temple University, Department of Biology, Philadelphia PA 19122, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, PA 19122, USA
| | - Sudhir Kumar
- Temple University, Department of Biology, Philadelphia PA 19122, USA
- Institute for Genomics and Evolutionary Medicine, Temple University, PA 19122, USA
| | - Jody Hey
- Temple University, Department of Biology, Philadelphia PA 19122, USA
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7
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Wakeley J, Fan WT(L, Koch E, Sunyaev S. Recurrent mutation in the ancestry of a rare variant. Genetics 2023; 224:iyad049. [PMID: 36967220 PMCID: PMC10324944 DOI: 10.1093/genetics/iyad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 01/30/2023] [Accepted: 03/08/2023] [Indexed: 03/28/2023] Open
Abstract
Recurrent mutation produces multiple copies of the same allele which may be co-segregating in a population. Yet, most analyses of allele-frequency or site-frequency spectra assume that all observed copies of an allele trace back to a single mutation. We develop a sampling theory for the number of latent mutations in the ancestry of a rare variant, specifically a variant observed in relatively small count in a large sample. Our results follow from the statistical independence of low-count mutations, which we show to hold for the standard neutral coalescent or diffusion model of population genetics as well as for more general coalescent trees. For populations of constant size, these counts are distributed like the number of alleles in the Ewens sampling formula. We develop a Poisson sampling model for populations of varying size and illustrate it using new results for site-frequency spectra in an exponentially growing population. We apply our model to a large data set of human SNPs and use it to explain dramatic differences in site-frequency spectra across the range of mutation rates in the human genome.
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Affiliation(s)
- John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Wai-Tong (Louis) Fan
- Department of Mathematics, Indiana University, Bloomington, IN 47405, USA
- Center of Mathematical Sciences and Applications, Harvard University, Cambridge, MA 02138, USA
| | - Evan Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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8
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Danilchenko VY, Zytsar MV, Maslova EA, Orishchenko KE, Posukh OL. Insight into the Natural History of Pathogenic Variant c.919-2A>G in the SLC26A4 Gene Involved in Hearing Loss: The Evidence for Its Common Origin in Southern Siberia (Russia). Genes (Basel) 2023; 14:genes14040928. [PMID: 37107686 PMCID: PMC10137394 DOI: 10.3390/genes14040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Pathogenic variants in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4), or Pendred syndrome, are some of the most common causes of hearing loss worldwide. Earlier, we found a high proportion of SLC26A4-related hearing loss with prevailing pathogenic variant c.919-2A>G (69.3% among all mutated SLC26A4 alleles that have been identified) in Tuvinian patients belonging to the indigenous Turkic-speaking Siberian people living in the Tyva Republic (Southern Siberia, Russia), which implies a founder effect in the accumulation of c.919-2A>G in Tuvinians. To evaluate a possible common origin of c.919-2A>G, we genotyped polymorphic STR and SNP markers, intragenic and flanking SLC26A4, in patients homozygous for c.919-2A>G and in healthy controls. The common STR and SNP haplotypes carrying c.919-2A>G were revealed, which convincingly indicates the origin of c.919-2A>G from a single ancestor, supporting a crucial role of the founder effect in the c.919-2A>G prevalence in Tuvinians. Comparison analysis with previously published data revealed the identity of the small SNP haplotype (~4.5 kb) in Tuvinian and Han Chinese carriers of c.919-2A>G, which suggests their common origin from founder chromosomes. We assume that c.919-2A>G could have originated in the geographically close territories of China or Tuva and subsequently spread to other regions of Asia. In addition, the time intervals of the c.919-2A>G occurrence in Tuvinians were roughly estimated.
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Affiliation(s)
- Valeriia Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Konstantin E Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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Aboagye ET, Adadey SM, Wonkam-Tingang E, Amenga-Etego L, Awandare GA, Wonkam A. Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment. Genes (Basel) 2023; 14:399. [PMID: 36833326 PMCID: PMC9957346 DOI: 10.3390/genes14020399] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.
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Affiliation(s)
- Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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Cohen ZP, François O, Schoville SD. Museum Genomics of an Agricultural Super-Pest, the Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae), Provides Evidence of Adaptation from Standing Variation. Integr Comp Biol 2022; 62:1827-1837. [PMID: 36036479 DOI: 10.1093/icb/icac137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 01/05/2023] Open
Abstract
Despite extensive research on agricultural pests, our knowledge about their evolutionary history is often limited. A mechanistic understanding of the demographic changes and modes of adaptation remains an important goal, as it improves our understanding of organismal responses to environmental change and our ability to sustainably manage pest populations. Emerging genomic datasets now allow for characterization of demographic and adaptive processes, but face limits when they are drawn from contemporary samples, especially in the context of strong demographic change, repeated selection, or adaptation involving modest shifts in allele frequency at many loci. Temporal sampling, however, can improve our ability to reconstruct evolutionary events. Here, we leverage museum samples to examine whether population genomic diversity and structure has changed over time, and to identify genomic regions that appear to be under selection. We focus on the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say 1824; Coleoptera: Chrysomelidae), which is widely regarded as a super-pest due to its rapid, and repeated, evolution to insecticides. By combining whole genome resequencing data from 78 museum samples with modern sampling, we demonstrate that CPB expanded rapidly in the 19th century, leading to a reduction in diversity and limited genetic structure from the Midwest to Northeast United States. Temporal genome scans provide extensive evidence for selection acting in resistant field populations in Wisconsin and New York, including numerous known insecticide resistance genes. We also validate these results by showing that known selective sweeps in modern populations are identified by our genome scan. Perhaps most importantly, temporal analysis indicates selection on standing genetic variation, as we find evidence for parallel evolution in the two geographical regions. Parallel evolution involves a range of phenotypic traits not previously identified as under selection in CPB, such as reproductive and morphological functional pathways that might be important for adaptation to agricultural habitats.
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Affiliation(s)
- Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA.,Insect Control and Cotton Disease Research Unit, USDA, Agricultural Research Service, College Station, TX, USA
| | | | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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11
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Muktupavela RA, Petr M, Ségurel L, Korneliussen T, Novembre J, Racimo F. Modeling the spatiotemporal spread of beneficial alleles using ancient genomes. eLife 2022; 11:e73767. [PMID: 36537881 PMCID: PMC9767474 DOI: 10.7554/elife.73767] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.
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Affiliation(s)
- Rasa A Muktupavela
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Martin Petr
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
| | - Laure Ségurel
- UMR5558 Biométrie et Biologie Evolutive, CNRS - Université Lyon 1VilleurbanneFrance
| | | | - John Novembre
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, GLOBE Institute, Faculty of HealthCopenhagenDenmark
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12
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Mansouri S, Gogoi H, Patel S, Katikaneni DS, Singh A, Aybar-Torres A, de Lartigue G, Jin L. MPYS Modulates Fatty Acid Metabolism and Immune Tolerance at Homeostasis Independent of Type I IFNs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2114-2132. [PMID: 36261171 PMCID: PMC9679991 DOI: 10.4049/jimmunol.2200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/15/2022] [Indexed: 01/04/2023]
Abstract
MPYS/STING (stimulator of IFN genes) senses cyclic dinucleotides (CDNs), generates type I IFNs, and plays a critical role in infection, inflammation, and cancer. In this study, analyzing genotype and haplotype data from the 1000 Genomes Project, we found that the R71H-G230A-R293Q (HAQ) MPYS allele frequency increased 57-fold in East Asians compared with sub-Saharan Africans. Meanwhile, the G230A-R293Q (AQ) allele frequency decreased by 98% in East Asians compared with sub-Saharan Africans. We propose that the HAQ and AQ alleles underwent a natural selection during the out-of-Africa migration. We used mouse models of HAQ and AQ to investigate the underlying mechanism. We found that the mice carrying the AQ allele, which disappeared in East Asians, had normal CDN-type I IFN responses. Adult AQ mice, however, had less fat mass than did HAQ or wild-type mice on a chow diet. AQ epididymal adipose tissue had increased regulatory T cells and M2 macrophages with protein expression associated with enhanced fatty acid oxidation. Conditional knockout mice and adoptive cell transfer indicate a macrophage and regulatory T cell-intrinsic role of MPYS in fatty acid metabolism. Mechanistically, AQ/IFNAR1-/- mice had a similar lean phenotype as for the AQ mice. MPYS intrinsic tryptophan fluorescence revealed that the R71H change increased MPYS hydrophilicity. Lastly, we found that the second transmembrane (TM) and the TM2-TM3 linker region of MPYS interact with activated fatty acid, fatty acyl-CoA. In summary, studying the evolution of the human MPYS gene revealed an MPYS function in modulating fatty acid metabolism that may be critical during the out-of-Africa migration.
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Affiliation(s)
- Samira Mansouri
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Himanshu Gogoi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Seema Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Divya S. Katikaneni
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Arashdeep Singh
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL; and
- Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, FL
| | - Alexandra Aybar-Torres
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Guillaume de Lartigue
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL; and
- Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, FL
| | - Lei Jin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL
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13
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Kitano J, Ishikawa A, Ravinet M, Courtier-Orgogozo V. Genetic basis of speciation and adaptation: from loci to causative mutations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200503. [PMID: 35634921 PMCID: PMC9149796 DOI: 10.1098/rstb.2020.0503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Laboratory of Molecular Ecological Genetics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8562, Japan
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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14
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Loeuillet C, Dhellemmes M, Cazin C, Kherraf ZE, Fourati Ben Mustapha S, Zouari R, Thierry-Mieg N, Arnoult C, Ray PF. A recurrent ZP1 variant is responsible for Oocyte Maturation Defect with degenerated oocytes in infertile females. Clin Genet 2022; 102:22-29. [PMID: 35460069 PMCID: PMC9327729 DOI: 10.1111/cge.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/08/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
A female factor is present in approximately 70% of couple infertility, often due to ovulatory disorders. In oocyte maturation defect (OMD), affected patients have a primary infertility with normal menstrual cycles but produce no oocyte, degenerated (atretic) or abnormal oocytes blocked at different stages of maturation. Four genes have so far been associated with OMD: PATL2, TUBB8, WEE2, and ZP1. In our initial study, 6 out of 23 OMD subjects were shown to carry the same PATL2 homozygous loss of function variant and one patient had a TUBB8 truncating variant. Here, we included four additional OMD patients and reanalyzed all 27 subjects. In addition to the seven patients with a previously identified defect, five carried the same deleterious homozygous ZP1 variant (c.1097G>A; p.Arg366Gln). All the oocytes from ZP1‐associated patients appeared shriveled and dark indicating that the abnormal ZP1 protein induced oocyte death and degeneration. Overall ZP1‐associated patients had degenerated or absent oocytes contrary to PATL2‐associated subjects who had immature oocytes blocked mainly at the germinal vesicle stage. In this cohort of North African OMD patients, whole exome sequencing permitted to diagnose 44% of the patients studied and to identify a new frequent ZP1 variant.
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Affiliation(s)
- Corinne Loeuillet
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Magali Dhellemmes
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Caroline Cazin
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, Grenoble, France.,Laboratoire Eurofins Biomnis, Département de Génétique Moléculaire, Lyon, France
| | - Zine-Eddine Kherraf
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | | | - Raoudha Zouari
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | | | - Christophe Arnoult
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Pierre F Ray
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
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15
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Ma Y, Wang X, Shoshany N, Jiao X, Lee A, Ku G, Baple EL, Fasham J, Nadeem R, Naeem MA, Riazuddin S, Riazuddin SA, Crosby AH, Hejtmancik JF. CLCC1 c. 75C>A Mutation in Pakistani Derived Retinitis Pigmentosa Families Likely Originated With a Single Founder Mutation 2,000-5,000 Years Ago. Front Genet 2022; 13:804924. [PMID: 35391798 PMCID: PMC8980549 DOI: 10.3389/fgene.2022.804924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: A CLCC1 c. 75C > A (p.D25E) mutation has been associated with autosomal recessive pigmentosa in patients in and from Pakistan. CLCC1 is ubiquitously expressed, and knockout models of this gene in zebrafish and mice are lethal in the embryonic period, suggesting that possible retinitis pigmentosa mutations in this gene might be limited to those leaving partial activity. In agreement with this hypothesis, the mutation is the only CLCC1 mutation associated with retinitis pigmentosa to date, and all identified patients with this mutation share a common SNP haplotype surrounding the mutation, suggesting a common founder. Methods: SNPs were genotyped by a combination of WGS and Sanger sequencing. The original founder haplotype, and recombination pathways were delineated by examination to minimize recombination events. Mutation age was estimated by four methods including an explicit solution, an iterative approach, a Bayesian approach and an approach based solely on ancestral segment lengths using high density SNP data. Results: All members of each of the nine families studied shared a single autozygous SNP haplotype for the CLCC1 region ranging from approximately 1–3.5 Mb in size. The haplotypes shared by the families could be derived from a single putative ancestral haplotype with at most two recombination events. Based on the haplotype and Gamma analysis, the estimated age of the founding mutation varied from 79 to 196 generations, or approximately 2,000–5,000 years, depending on the markers used in the estimate. The DMLE (Bayesian) estimates ranged from 2,160 generations assuming a population growth rate of 0–309 generations assuming a population growth rate of 2% with broad 95% confidence intervals. Conclusion: These results provide insight into the origin of the CLCC1 mutation in the Pakistan population. This mutation is estimated to have occurred 2000–5,000 years ago and has been transmitted to affected families of Pakistani origin in geographically dispersed locations around the world. This is the only mutation in CLCC1 identified to date, suggesting that the CLCC1 gene is under a high degree of constraint, probably imposed by functional requirements for this gene during embryonic development.
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Affiliation(s)
- Yan Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Xun Wang
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Nadav Shoshany
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States.,Matlow's Ophthalmo-genetic Laboratory, Shamir Medical Center, Zeriffin, Israel
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Adrian Lee
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
| | - Gregory Ku
- Diabetes Center, University of California, San Francisco, San Francisco, CA, United States
| | - Emma L Baple
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree), Gladstone Road, Exeter, United Kingdom
| | - James Fasham
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree), Gladstone Road, Exeter, United Kingdom
| | - Raheela Nadeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrew H Crosby
- Research, Innovation, Learning and Development (RILD) Wellcome Wolfson Centre, College of Medicine and Health, University of Exeter Medical School, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, United States
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16
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Quiver MH, Lachance J. Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. HGG ADVANCES 2022; 3:100083. [PMID: 35047867 PMCID: PMC8756519 DOI: 10.1016/j.xhgg.2021.100083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Large numbers of expression quantitative trait loci (eQTLs) have recently been identified in humans, and many of these regulatory variants have large allele frequency differences between populations. Here, we conducted genome-wide scans of selection to identify adaptive eQTLs (i.e., eQTLs with large population branch statistics). We then tested if tissue pleiotropy affects whether eQTLs are more or less likely to be adaptive and identified tissues that have been key targets of positive selection during the last 100,000 years. Top adaptive eQTL outliers include rs1043809, rs66899053, and rs2814778 (a SNP that is associated with malaria resistance). We found that effect sizes of eQTLs were negatively correlated with population branch statistics and that adaptive eQTLs affect two-thirds as many tissues as do non-adaptive eQTLs. Because the tissue breadth of an eQTL can be viewed as a measure of pleiotropy, these results imply that pleiotropy inhibits adaptation. The proportion of eQTLs that are adaptive varies by tissue, and we found that eQTLs that regulate expression in testis, thyroid, blood, or sun-exposed skin are enriched for signatures of positive selection. By contrast, eQTLs that regulate expression in the cerebrum or female-specific tissues have a relative lack of adaptive outliers. Scans of selections also reveal that many adaptive eQTLs are closely linked to disease-associated loci. Taken together, our results indicate that eQTLs have played an important role in recent human evolution.
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Affiliation(s)
- Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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17
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Chong Y, Jiang X, Liu G. An ancient positively selected BMPRIB missense variant increases litter size of Mongolian sheep populations following latitudinal gradient. Mol Genet Genomics 2022; 297:155-167. [PMID: 35013854 DOI: 10.1007/s00438-021-01828-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022]
Abstract
New gene mutation origination is a driving force for the evolution of organisms. The effect of FecB mutation in BMPRIB gene on the litter size of sheep has been well known for a long time, each copy of the mutant allele increases litter size by 0.4-0.5. However, the origin and adaptive evolution mechanism of FecB mutation are still unclear. Here we carried on the thorough analysis on evolutionary features of BMPRIB gene and found that 150 species as a whole is under purifying selection while sheep lineage shows evidence of positive selection. The results of allele age estimation revealed that the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago. Due the two shape drops in temperature subsequently, Mongolian sheep migrated from north to south following the northern nomadic people. Accordingly, the FecB mutant allele frequency increased, with the lowest in sheep locating at Mongolian plateau (0.01) and the highest in sheep locating at Yangtze River valley (0.96). In conclusion, the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago, and the differentiated litter size of Mongolian sheep might be the result of adaptation to various environments during the migration following latitudinal gradient. This study may well exemplify selection on an ancient variation triggered by drastic ecological shifts, and is also helpful to analyze the adaptive evolution mechanism of economic traits of domestic animals and identify major genes and molecular markers.
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Affiliation(s)
- Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China.
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18
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Sticca EL, Belbin GM, Gignoux CR. Current Developments in Detection of Identity-by-Descent Methods and Applications. Front Genet 2021; 12:722602. [PMID: 34567074 PMCID: PMC8461052 DOI: 10.3389/fgene.2021.722602] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 01/23/2023] Open
Abstract
Identity-by-descent (IBD), the detection of shared segments inherited from a common ancestor, is a fundamental concept in genomics with broad applications in the characterization and analysis of genomes. While historically the concept of IBD was extensively utilized through linkage analyses and in studies of founder populations, applications of IBD-based methods subsided during the genome-wide association study era. This was primarily due to the computational expense of IBD detection, which becomes increasingly relevant as the field moves toward the analysis of biobank-scale datasets that encompass individuals from highly diverse backgrounds. To address these computational barriers, the past several years have seen new methodological advances enabling IBD detection for datasets in the hundreds of thousands to millions of individuals, enabling novel analyses at an unprecedented scale. Here, we describe the latest innovations in IBD detection and describe opportunities for the application of IBD-based methods across a broad range of questions in the field of genomics.
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Affiliation(s)
- Evan L Sticca
- Human Medical Genetics and Genomics Program and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gillian M Belbin
- Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christopher R Gignoux
- Human Medical Genetics and Genomics Program and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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19
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The Aldehyde Dehydrogenase ALDH2*2 Allele, Associated with Alcohol Drinking Behavior, Dates Back to Prehistoric Times. Biomolecules 2021; 11:biom11091376. [PMID: 34572589 PMCID: PMC8465343 DOI: 10.3390/biom11091376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 01/02/2023] Open
Abstract
Human alcohol-consumption behavior is partly genetically encoded. The alcohol consumption of 987 residents in Keelung, Taiwan, was evaluated by using the Alcohol Use Disorder Identification Test (AUDIT). We assessed ~750,000 genomic variants of 71 residents who drank hazardously (AUDIT score ≥ 8) and 126 residents who did not drink in their daily lives (AUDIT score = 0), using high-density single nucleotide polymorphism (SNP) arrays. The rs671 G > A manifests the highest significance of the association with drinking behavior (Fisher’s exact P = 8.75 × 10−9). It is a pleiotropic, non-synonymous variant in the aldehyde dehydrogenase 2 (ALDH2) gene. The minor allele “A”, commonly known as ALDH2*2, is associated with non-drinkers. Intriguingly, identity-by-descent haplotypes encompassing genomic regions with a median length of 1.6 (0.6–2.0) million nucleotide bases were found in all study participants with either heterozygous or homozygous ALDH2*2 (n = 81 and 13, respectively). We also analyzed a public-domain dataset with genome-wide genotypes of 2000 participants in Guangzhou, a coastal city in Southern China. Among them, 175 participants have homozygous ALDH2*2 genotype, and again, long ALDH2*2-carrying haplotypes were found in all 175 participants without exceptions. The median length of the ALDH2*2-carrying haplotype is 1.7 (0.5–2.8) million nucleotide bases. The haplotype lengths in the Keelung and Guangzhou cohorts combined indicate that the origin of the ALDH2*2 allele dates back to 7935 (7014–9381) years ago. In conclusion, the rs671 G > A is the leading genomic variant associated with the long-term drinking behavior among residents of Keelung, Taiwan. The ALDH2*2 allele has been in Asian populations since prehistoric times.
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20
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Liu C, Jiang X, Chi S, Bo D, Liu G. Contribution of the mutation T865G in TPH1 gene to the genetic potentiality of housed Mongolian sheep to year-round breeding. Reprod Domest Anim 2021; 56:1406-1412. [PMID: 34390051 DOI: 10.1111/rda.14005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/13/2023]
Abstract
Seasonal breeding is widespread in sheep and significantly affects the development of the housed sheep industry. To improve and balance the reproduction performance of sheep, year-round breeding has the goal of modern sheep farming. The tryptophan hydroxylase (TPH), which initiates and regulates biosynthesis of melatonin, is an important player in the formation of mammalian year-round breeding. However, little is known about its role in regulation of sheep seasonal breeding. In this study, a missense mutation, T865G in TPH1 gene was detected in 328 individuals of six Mongolian sheep groups. It was positively selected among Mongolian sheep. This mutation may appear between 13,683 and 350,973 years ago and only exist in Hu sheep now. In Hu sheep, the frequency of allele T was 89.66%, and that of allele G was 10.34%. The TPH1 protein structure and property analysis suggested that this mutation from T to G affect the three-dimensional structure and reduce the hydropathicity of catalytic core. When the allele is T, the protein activity is twice that of the allele G, and their difference was significant (p < .05). In conclusion, T865G is an ancient mutation of TPH1 gene and affects the function of TPH protein, which may contribute to the genetic potentiality of Mongolian sheep to year-round breeding.
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Affiliation(s)
- Chenhui Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China.,Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Shaxuan Chi
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Dongdong Bo
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
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21
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Riddiford N, Siudeja K, van den Beek M, Boumard B, Bardin AJ. Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells. Genome Res 2021; 31:1419-1432. [PMID: 34168010 PMCID: PMC8327918 DOI: 10.1101/gr.268441.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 06/15/2021] [Indexed: 12/15/2022]
Abstract
Spontaneous mutations can alter tissue dynamics and lead to cancer initiation. Although large-scale sequencing projects have illuminated processes that influence somatic mutation and subsequent tumor evolution, the mutational dynamics operating in the very early stages of cancer development are currently not well understood. To explore mutational processes in the early stages of cancer evolution, we exploited neoplasia arising spontaneously in the Drosophila intestine. Analysing whole-genome sequencing data with a dedicated bioinformatic pipeline, we found neoplasia formation to be driven largely through the inactivation of Notch by structural variants, many of which involve highly complex genomic rearrangements. The genome-wide mutational burden in neoplasia was found to be similar to that of several human cancers. Finally, we identified genomic features associated with spontaneous mutation, and defined the evolutionary dynamics and mutational landscape operating within intestinal neoplasia over the short lifespan of the adult fly. Our findings provide unique insight into mutational dynamics operating over a short timescale in the genetic model system, Drosophila melanogaster.
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Affiliation(s)
- Nick Riddiford
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Katarzyna Siudeja
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Marius van den Beek
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Benjamin Boumard
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75005 Paris, France
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Cazin C, Boumerdassi Y, Martinez G, Fourati Ben Mustapha S, Whitfield M, Coutton C, Thierry-Mieg N, Di Pizio P, Rives N, Arnoult C, Touré A, Ray PF, Zouari R, Sifer C, Kherraf ZE. Identification and Characterization of the Most Common Genetic Variant Responsible for Acephalic Spermatozoa Syndrome in Men Originating from North Africa. Int J Mol Sci 2021; 22:ijms22042187. [PMID: 33671757 PMCID: PMC7927044 DOI: 10.3390/ijms22042187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
Acephalic spermatozoa syndrome (ASS) is a rare but extremely severe type of teratozoospermia, defined by the presence of a majority of headless flagella and a minority of tail-less sperm heads in the ejaculate. Like the other severe monomorphic teratozoospermias, ASS has a strong genetic basis and is most often caused by bi-allelic variants in SUN5 (Sad1 and UNC84 domain-containing 5). Using whole exome sequencing (WES), we investigated a cohort of nine infertile subjects displaying ASS. These subjects were recruited in three centers located in France and Tunisia, but all originated from North Africa. Sperm from subjects carrying candidate genetic variants were subjected to immunofluorescence analysis and transmission electron microscopy. Moreover, fluorescent in situ hybridization (FISH) was performed on sperm nuclei to assess their chromosomal content. Variant filtering permitted us to identify the same SUN5 homozygous frameshift variant (c.211+1_211+2dup) in 7/9 individuals (78%). SUN5 encodes a protein localized on the posterior part of the nuclear envelope that is necessary for the attachment of the tail to the sperm head. Immunofluorescence assays performed on sperm cells from three mutated subjects revealed a total absence of SUN5, thus demonstrating the deleterious impact of the identified variant on protein expression. Transmission electron microscopy showed a conserved flagellar structure and a slightly decondensed chromatin. FISH did not highlight a higher rate of chromosome aneuploidy in spermatozoa from SUN5 patients compared to controls, indicating that intra-cytoplasmic sperm injection (ICSI) can be proposed for patients carrying the c.211+1_211+2dup variant. These results suggest that the identified SUN5 variant is the main cause of ASS in the North African population. Consequently, a simple and inexpensive genotyping of the 211+1_211+2dup variant could be beneficial for affected men of North African origin before resorting to more exhaustive genetic analyses.
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Affiliation(s)
- Caroline Cazin
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
- UM GI-DPI, CHU Grenoble Alpes, F-38000 Grenoble, France
| | - Yasmine Boumerdassi
- Department of Reproductive Biology, Hôpital Jean Verdier, Assistance Publique, Hôpitaux de Paris, F-75004 Paris, France; (Y.B.); (C.S.)
| | - Guillaume Martinez
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
- UM de Génétique Chromosomique, CHU Grenoble Alpes, F-38000 Grenoble, France
| | - Selima Fourati Ben Mustapha
- Centre d’Aide Médicale à la Procréation, Polyclinique les Jasmin, Centre Urbain Nord, Tunis 1003, Tunisia; (S.F.B.M.); (R.Z.)
| | - Marjorie Whitfield
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
| | - Charles Coutton
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
- Department of Reproductive Biology, Hôpital Jean Verdier, Assistance Publique, Hôpitaux de Paris, F-75004 Paris, France; (Y.B.); (C.S.)
| | | | - Pierre Di Pizio
- EA 4308 ‘Gametogenesis and Gamete Quality, Normandie University, UNIROUEN, F-76000 Rouen, France; (P.D.P.); (N.R.)
- Reproductive Biology Laboratory-CECOS, Assisted Reproductive Center, Rouen Normandy University Hospital, F-76000 Rouen, France
| | - Nathalie Rives
- EA 4308 ‘Gametogenesis and Gamete Quality, Normandie University, UNIROUEN, F-76000 Rouen, France; (P.D.P.); (N.R.)
- Reproductive Biology Laboratory-CECOS, Assisted Reproductive Center, Rouen Normandy University Hospital, F-76000 Rouen, France
| | - Christophe Arnoult
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
| | - Aminata Touré
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
| | - Pierre F. Ray
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
- UM GI-DPI, CHU Grenoble Alpes, F-38000 Grenoble, France
| | - Raoudha Zouari
- Centre d’Aide Médicale à la Procréation, Polyclinique les Jasmin, Centre Urbain Nord, Tunis 1003, Tunisia; (S.F.B.M.); (R.Z.)
| | - Christophe Sifer
- Department of Reproductive Biology, Hôpital Jean Verdier, Assistance Publique, Hôpitaux de Paris, F-75004 Paris, France; (Y.B.); (C.S.)
| | - Zine-Eddine Kherraf
- Institute for Advanced Biosciences, INSERM, CNRS, Université Grenoble Alpes, F-38000 Grenoble, France; (C.C.); (G.M.); (M.W.); (C.C.); (C.A.); (A.T.); (P.F.R.)
- UM GI-DPI, CHU Grenoble Alpes, F-38000 Grenoble, France
- Correspondence:
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Bereczky Z, Gindele R, Fiatal S, Speker M, Miklós T, Balogh L, Mezei Z, Szabó Z, Ádány R. Age and Origin of the Founder Antithrombin Budapest 3 (p.Leu131Phe) Mutation; Its High Prevalence in the Roma Population and Its Association With Cardiovascular Diseases. Front Cardiovasc Med 2021; 7:617711. [PMID: 33614741 PMCID: PMC7892435 DOI: 10.3389/fcvm.2020.617711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Antithrombin (AT) is one of the most important regulator of hemostasis. AT Budapest 3 (ATBp3) is a prevalent type II heparin-binding site (IIHBS) deficiency due to founder effect. Thrombosis is a complex disease including arterial (ATE) and venous thrombotic events (VTE) and the Roma population, the largest ethnic minority in Europe has increased susceptibility to these diseases partly due to their unfavorable genetic load. We aimed to calculate the age and origin of ATBp3 and to explore whether the frequency of it is higher in the Roma population as compared with the general population from the corresponding geographical area. We investigated the association of ATBp3 with thrombotic events in well-defined patients' populations in order to refine the recommendation when testing for ATBp3 is useful. Methods and Results: Prevalence of ATBp3, investigated in large samples (n = 1,000 and 1,185 for general Hungarian and Roma populations, respectively) was considerably high, almost 3%, among Roma and the founder effect was confirmed in their samples, while it was absent in the Hungarian general population. Age of ATBp3—as calculated by analysis of 8 short tandem repeat sequences surrounding SERPINC1—was dated back to XVII Century, when Roma migration in Central and Eastern Europe occurred. In our IIHBS cohort (n = 230), VTE was registered in almost all ATBp3 homozygotes (93%) and in 44% of heterozygotes. ATE occurred with lower frequency in ATBp3 (around 6%); it was rather associated with AT Basel (44%). All patients with ATE were young at the time of diagnosis. Upon investigating consecutive young (<40 years) patients with ATE (n = 92) and VTE (n = 110), the presence of ATBp3 was remarkable. Conclusions: ATBp3, a 400-year-old founder mutation is prevalent in Roma population and its Roma origin can reasonably be assumed. By the demonstration of the presence of ATBp3 in ATE patients, we draw the attention to consider type IIHBS AT deficiency in the background of not only VTE but also ATE, especially in selected populations as young patients without advanced atherosclerosis. We recommend including the investigation of ATBp3 as part of thrombosis risk assessment and stratification in Roma individuals.
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Affiliation(s)
- Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Réka Gindele
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilvia Fiatal
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Marianna Speker
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tünde Miklós
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Balogh
- Department of Cardiology and Cardiovascular Surgery, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltán Mezei
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsuzsanna Szabó
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Magyar Tudományos Akadémia - Debrecen Public Health Research Group, University of Debrecen, Debrecen, Hungary
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He Z, Dai X, Beaumont M, Yu F. Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach. Genetics 2020; 216:463-480. [PMID: 32769100 PMCID: PMC7536852 DOI: 10.1534/genetics.120.303400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/29/2020] [Indexed: 11/18/2022] Open
Abstract
Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.
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Affiliation(s)
- Zhangyi He
- Department of Statistics, University of Oxford, OX1 3LB, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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High Rates of Three Common GJB2 Mutations c.516G>C, c.-23+1G>A, c.235delC in Deaf Patients from Southern Siberia Are Due to the Founder Effect. Genes (Basel) 2020; 11:genes11070833. [PMID: 32708339 PMCID: PMC7397271 DOI: 10.3390/genes11070833] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/17/2022] Open
Abstract
The mutations in the GJB2 gene (13q12.11, MIM 121011) encoding transmembrane protein connexin 26 (Cx26) account for a significant portion of hereditary hearing loss worldwide. Earlier we found a high prevalence of recessive GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous Turkic-speaking Siberian peoples (Tuvinians and Altaians) from the Tyva Republic and Altai Republic (Southern Siberia, Russia) and proposed the founder effect as a cause for their high rates in these populations. To reconstruct the haplotypes associated with each of these mutations, the genotyping of polymorphic genetic markers both within and flanking the GJB2 gene was performed in 28 unrelated individuals homozygous for c.516G>C (n = 18), c.-23+1G>A (n = 6), or c.235delC (n = 4) as well as in the ethnically matched controls (62 Tuvinians and 55 Altaians) without these mutations. The common haplotypes specific for mutations c.516G>C, c.-23+1G>A, or c.235delC were revealed implying a single origin of each of these mutations. The age of mutations estimated by the DMLE+ v2.3 software and the single marker method is discussed in relation to ethnic history of Tuvinians and Altaians. The data obtained in this study support a crucial role of the founder effect in the high prevalence of GJB2 mutations c.516G>C, c.-23+1G>A, c.235delC in indigenous populations of Southern Siberia.
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26
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Nishiyama KV, Satta Y, Gojobori J. Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally? Genes (Basel) 2020; 11:genes11060658. [PMID: 32560373 PMCID: PMC7349701 DOI: 10.3390/genes11060658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/13/2020] [Accepted: 06/13/2020] [Indexed: 12/29/2022] Open
Abstract
Dyslexia, or reading disability, is found to have a genetic basis, and several related genes have been reported. We investigated whether natural selection has acted on single nucleotide polymorphisms (SNPs) that were reported to be associated with risk/non-risk for the reading disability of Chinese characters. We applied recently developed 2D SFS-based statistics to SNP data of East Asian populations to examine whether there is any sign of selective sweep. While neutrality was not rejected for most SNPs, significant signs of selection were detected for two linkage disequilibrium (LD) regions containing the reported SNPs of GNPTAB and DCDC2. Furthermore, we searched for a selection target site among the SNPs in these LD regions, because a causal site is not necessarily a reported SNP but could instead be a tightly linked site. In both LD regions, we found candidate target sites, which may have an effect on expression regulation and have been selected, although which genes these SNPs affect remains unknown. Because most people were not engaged in reading until recently, it is unlikely that there has been selective pressure on reading ability itself. Consistent with this, our results suggest a possibility of genetic hitchhiking, whereby alleles of the reported SNPs may have increased in frequency together with the selected target, which could have functions for other genes and traits apart from reading ability.
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27
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Papamentzelopoulou M, Apostolou P, Fostira F, Dimitrakakis C, Loutradis D, Fountzilas G, Yannoukakos D, Konstantopoulou I. Prevalence and founder effect of the BRCA1 p.(Val1833Met) variant in the Greek population, with further evidence for pathogenicity and risk modification. Cancer Genet 2019; 237:90-96. [PMID: 31447071 DOI: 10.1016/j.cancergen.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/31/2019] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE Multiple lines of evidence have suggested a likely causative role in breast/ovarian cancer (BrCa/OvCa) predisposition for the BRCA1 p.(Val1833Met) variant, predominantly found among Greek patients. Our aim was to study the variant's prevalence and founder effect on the Greek population, while providing additional data for its pathogenicity. METHODS We genotyped 3531 BrCa/OvCa patients using Sanger and next generation sequencing, as well as 1558 healthy, age-matched females with real-time PCR. Carriers underwent haplotype analysis to determine a founder effect. A co-segregation analysis was applied to estimate the likelihood ratio for pathogenicity. RESULTS In total, 27 BrCa/OvCa patients (0.77%; 27/3531) were found to carry the p.(Val1833Met) variant. No carriers were identified in the control group diagnosis. A common shared haplotype, spanning 2.76 Mb on chromosome 17 was demonstrated among carriers, establishing the founder effect. BRCA1, p.(Val1833Met) is possibly a disease-associated variant, supported by a likelihood ratio of 1.88, while a correlation to ovarian cancer is suspected. CONCLUSIONS Altogether, BRCA1, p.(Val1833Met) variant is a Greek founder and is very likely to predispose for BrCa/OvCa. Therefore, such carriers should be counselled accordingly, with clinical recommendations supporting surveillance and risk-reduction strategies, while providing the option for targeted therapeutic interventions.
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Affiliation(s)
- Myrto Papamentzelopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | | | - Dimitris Loutradis
- 1st Department of Obstetrics and Gynecology, Athens University Medical School, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece.
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Platt A, Pivirotto A, Knoblauch J, Hey J. An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations. PLoS Genet 2019; 15:e1008340. [PMID: 31425500 PMCID: PMC6715256 DOI: 10.1371/journal.pgen.1008340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/29/2019] [Accepted: 08/01/2019] [Indexed: 11/18/2022] Open
Abstract
Allele age has long been a focus of population genetic research, primarily because it can be an important clue to the fitness effects of an allele. By virtue of their effects on fitness, alleles under directional selection are expected to be younger than neutral alleles of the same frequency. We developed a new coalescent-based estimator of a close proxy for allele age, the time when a copy of an allele first shares common ancestry with other chromosomes in a sample not carrying that allele. The estimator performs well, including for the very rarest of alleles that occur just once in a sample, with a bias that is typically negative. The estimator is mostly insensitive to population demography and to factors that can arise in population genomic pipelines, including the statistical phasing of chromosomes. Applications to 1000 Genomes Data and UK10K genome data confirm predictions that singleton alleles that alter proteins are significantly younger than those that do not, with a greater difference in the larger UK10K dataset, as expected. The 1000 Genomes populations varied markedly in their distributions for singleton allele ages, suggesting that these distributions can be used to inform models of demographic history, including recent events that are only revealed by their impacts on the ages of very rare alleles.
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Affiliation(s)
- Alexander Platt
- Center for Computational Genetics and Genomics, Dept. Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Alyssa Pivirotto
- Center for Computational Genetics and Genomics, Dept. Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jared Knoblauch
- Center for Computational Genetics and Genomics, Dept. Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jody Hey
- Center for Computational Genetics and Genomics, Dept. Biology, Temple University, Philadelphia, Pennsylvania, United States of America
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29
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Caron H, Molino J, Sabatier D, Léger P, Chaumeil P, Scotti‐Saintagne C, Frigério J, Scotti I, Franc A, Petit RJ. Chloroplast DNA variation in a hyperdiverse tropical tree community. Ecol Evol 2019; 9:4897-4905. [PMID: 31031952 PMCID: PMC6476754 DOI: 10.1002/ece3.5096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 02/11/2019] [Accepted: 03/01/2019] [Indexed: 01/05/2023] Open
Abstract
We investigate chloroplast DNA variation in a hyperdiverse community of tropical rainforest trees in French Guiana, focusing on patterns of intraspecific and interspecific variation. We test whether a species genetic diversity is higher when it has congeners in the community with which it can exchange genes and if shared haplotypes are more frequent in genetically diverse species, as expected in the presence of introgression.We sampled a total of 1,681 individual trees from 472 species corresponding to 198 genera and sequenced them at a noncoding chloroplast DNA fragment.Polymorphism was more frequent in species that have congeneric species in the study site than in those without congeners (30% vs. 12%). Moreover, more chloroplast haplotypes were shared with congeners in polymorphic species than in monomorphic ones (44% vs. 28%).Despite large heterogeneities caused by genus-specific behaviors in patterns of hybridization, these results suggest that the higher polymorphism in the presence of congeners is caused by local introgression rather than by incomplete lineage sorting. Our findings suggest that introgression has the potential to drive intraspecific genetic diversity in species-rich tropical forests.
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Affiliation(s)
- Henri Caron
- BIOGECOINRA, Univ. BordeauxCestasFrance
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
| | | | - Daniel Sabatier
- AMAP, IRD, Cirad, CNRS, INRAUniversité de MontpellierMontpellierFrance
| | | | | | - Caroline Scotti‐Saintagne
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
- INRA, UR629 Ecologie des Forêts MéditerranéennesURFMAvignonFrance
| | | | - Ivan Scotti
- INRAUMR 0745 EcoFoG (Ecologie des forêts de Guyane)KourouFrance
- INRA, UR629 Ecologie des Forêts MéditerranéennesURFMAvignonFrance
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Kim MS, Patel KP, Teng AK, Berens AJ, Lachance J. Genetic disease risks can be misestimated across global populations. Genome Biol 2018; 19:179. [PMID: 30424772 PMCID: PMC6234640 DOI: 10.1186/s13059-018-1561-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. Here, we integrate whole genome sequence data from global populations, results from thousands of genome-wide association studies (GWAS), and extensive computer simulations to identify how genetic disease risks can be misestimated. RESULTS In contrast to null expectations, we find that risk allele frequencies at known disease loci are significantly different for African populations compared to other continents. Strikingly, ancestral risk alleles are found at 9.51% higher frequency in Africa, and derived risk alleles are found at 5.40% lower frequency in Africa. By simulating GWAS with different study populations, we find that non-African cohorts yield disease associations that have biased allele frequencies and that African cohorts yield disease associations that are relatively free of bias. We also find empirical evidence that genotyping arrays and SNP ascertainment bias contribute to continental differences in risk allele frequencies. Because of these causes, polygenic risk scores can be grossly misestimated for individuals of African descent. Importantly, continental differences in risk allele frequencies are only moderately reduced if GWAS use whole genome sequences and hundreds of thousands of cases and controls. Finally, comparisons between uncorrected and corrected genetic risk scores reveal the benefits of considering whether risk alleles are ancestral or derived. CONCLUSIONS Our results imply that caution must be taken when extrapolating GWAS results from one population to predict disease risks in another population.
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Affiliation(s)
- Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Kane P Patel
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Andrew K Teng
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Ali J Berens
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA.
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Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 2018; 10:304-318. [PMID: 29281015 PMCID: PMC5786231 DOI: 10.1093/gbe/evx276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 01/05/2023] Open
Abstract
Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, California
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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32
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A Homozygous Ancestral SVA-Insertion-Mediated Deletion in WDR66 Induces Multiple Morphological Abnormalities of the Sperm Flagellum and Male Infertility. Am J Hum Genet 2018; 103:400-412. [PMID: 30122540 DOI: 10.1016/j.ajhg.2018.07.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023] Open
Abstract
Multiple morphological abnormalities of the sperm flagellum (MMAF) is a severe form of male infertility defined by the presence of a mosaic of anomalies, including short, bent, curled, thick, or absent flagella, resulting from a severe disorganization of the axoneme and of the peri-axonemal structures. Mutations in DNAH1, CFAP43, and CFAP44, three genes encoding axoneme-related proteins, have been described to account for approximately 30% of the MMAF cases reported so far. Here, we searched for pathological copy-number variants in whole-exome sequencing data from a cohort of 78 MMAF-affected subjects to identify additional genes associated with MMAF. In 7 of 78 affected individuals, we identified a homozygous deletion that removes the two penultimate exons of WDR66 (also named CFAP251), a gene coding for an axonemal protein preferentially localized in the testis and described to localize to the calmodulin- and spoke-associated complex at the base of radial spoke 3. Sequence analysis of the breakpoint region revealed in all deleted subjects the presence of a single chimeric SVA (SINE-VNTR-Alu) at the breakpoint site, suggesting that the initial deletion event was potentially mediated by an SVA insertion-recombination mechanism. Study of Trypanosoma WDR66's ortholog (TbWDR66) highlighted high sequence and structural analogy with the human protein and confirmed axonemal localization of the protein. Reproduction of the human deletion in TbWDR66 impaired flagellar movement, thus confirming WDR66 as a gene associated with the MMAF phenotype and highlighting the importance of the WDR66 C-terminal region.
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33
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Cooke NP, Nakagome S. Fine-tuning of Approximate Bayesian Computation for human population genomics. Curr Opin Genet Dev 2018; 53:60-69. [PMID: 30029009 DOI: 10.1016/j.gde.2018.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/30/2018] [Indexed: 12/13/2022]
Abstract
Approximate Bayesian Computation (ABC) is a flexible statistical tool widely applied to addressing a variety of questions regarding the origin and evolution of humans. The significant growth of genomic scale data from diverse geographic populations has facilitated the use of ABC in modelling the complex processes that underlie human demography and local adaptation. However, a fundamental issue still remains in how to efficiently capture patterns of genetic variation with a set of summary statistics in order to achieve better approximation of Bayesian inference. Here, we review recent advances in ABC methodology and its applications for human population genomics, with a particular focus on optimal tuning of ABC approaches for different types of genetic data and different sets of evolutionary parameters.
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Affiliation(s)
- Niall P Cooke
- Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, Dublin, Ireland.
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34
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Satta Y, Fujito NT, Takahata N. Nonequilibrium Neutral Theory for Hitchhikers. Mol Biol Evol 2018; 35:1362-1365. [PMID: 29722819 DOI: 10.1093/molbev/msy093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Selective sweep is a phenomenon of reduced variation at presumably neutrally evolving sites (hitchhikers) in the genome that is caused by the spread of a selected allele at a linked focal site, and is widely used to test for action of positive selection. Nonetheless, selective sweep may also provide an unprecedented opportunity for studying nonequilibrium properties of the neutral variation itself. We have demonstrated this possibility in relation to ancient selective sweep for modern human-specific changes and ongoing selective sweep for local population-specific changes.
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Affiliation(s)
- Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Naoko T Fujito
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Naoyuki Takahata
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
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35
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Abstract
The haplotypes of a beneficial allele carry information about its history that can shed light on its age and the putative cause for its increase in frequency. Specifically, the signature of an allele's age is contained in the pattern of variation that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to approaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to estimate the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.
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Affiliation(s)
- Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Graham Coop
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, Davis, CA
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL
- Department of Statistics, University of Chicago, Chicago, IL
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
- Department of Human Genetics, University of Chicago, Chicago, IL
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36
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Zonato V, Vanin S, Costa R, Tauber E, Kyriacou CP. Inverse European Latitudinal Cline at the timeless Locus of Drosophila melanogaster Reveals Selection on a Clock Gene: Population Genetics of ls-tim. J Biol Rhythms 2017; 33:15-23. [PMID: 29183263 DOI: 10.1177/0748730417742309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The spread of adaptive genetic variants in populations is a cornerstone of evolutionary theory but with relatively few biologically well-understood examples. Previous work on the ls-tim variant of timeless, which encodes the light-sensitive circadian regulator in Drosophila melanogaster, suggests that it may have originated in southeastern Italy. Flies characterized by the new allele show photoperiod-related phenotypes likely to be adaptive in seasonal environments. ls-tim may be spreading from its point of origin in Italy by directional selection, but there are alternative explanations for its observed clinal geographical distribution, including balancing selection and demography. From population analyses of ls-tim frequencies collected on the eastern side of the Iberian Peninsula, we show that ls-tim frequencies are inverted compared with those in Italy. This pattern is consistent with a scenario of directional selection rather than latitude-associated balancing selection. Neutrality tests further reveal the signature of directional selection at the ls-tim site, which is reduced a few kb pairs either side of ls-tim. A reanalysis of allele frequencies from a large number of microsatellite loci do not demonstrate any frequent ls-tim-like spatial patterns, so a general demographic effect or population expansion from southeastern Italy cannot readily explain current ls-tim frequencies. Finally, a revised estimate of the age of ls-tim allele using linkage disequilibrium and coalescent-based approaches reveals that it may be only 300 to 3000 years old, perhaps explaining why it has not yet gone to fixation. ls-tim thus provides a rare temporal snapshot of a new allele that has come under selection before it reaches equilibrium.
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Affiliation(s)
- Valeria Zonato
- Department of Genetics, University of Leicester, Leicester, UK
| | - Stefano Vanin
- Department of Biology, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy
| | - Eran Tauber
- Department of Genetics, University of Leicester, Leicester, UK.,Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
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37
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De Sanctis B, Krukov I, de Koning APJ. Allele Age Under Non-Classical Assumptions is Clarified by an Exact Computational Markov Chain Approach. Sci Rep 2017; 7:11869. [PMID: 28928413 PMCID: PMC5605573 DOI: 10.1038/s41598-017-12239-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/06/2017] [Indexed: 11/29/2022] Open
Abstract
Determination of the age of an allele based on its population frequency is a well-studied problem in population genetics, for which a variety of approximations have been proposed. We present a new result that, surprisingly, allows the expectation and variance of allele age to be computed exactly (within machine precision) for any finite absorbing Markov chain model in a matter of seconds. This approach makes none of the classical assumptions (e.g., weak selection, reversibility, infinite sites), exploits modern sparse linear algebra techniques, integrates over all sample paths, and is rapidly computable for Wright-Fisher populations up to Ne = 100,000. With this approach, we study the joint effect of recurrent mutation, dominance, and selection, and demonstrate new examples of “selective strolls” where the classical symmetry of allele age with respect to selection is violated by weakly selected alleles that are older than neutral alleles at the same frequency. We also show evidence for a strong age imbalance, where rare deleterious alleles are expected to be substantially older than advantageous alleles observed at the same frequency when population-scaled mutation rates are large. These results highlight the under-appreciated utility of computational methods for the direct analysis of Markov chain models in population genetics.
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Affiliation(s)
- Bianca De Sanctis
- University of Calgary, Cumming School of Medicine, Dept. of Biochemistry and Molecular Biology, Calgary, Alberta, Canada
| | - Ivan Krukov
- University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology Graduate Program (Bioinformatics stream), Calgary, Alberta, Canada
| | - A P Jason de Koning
- University of Calgary, Cumming School of Medicine, Dept. of Biochemistry and Molecular Biology, Calgary, Alberta, Canada. .,University of Calgary, Cumming School of Medicine, Department of Biochemistry and Molecular Biology Graduate Program (Bioinformatics stream), Calgary, Alberta, Canada. .,University of Calgary, Cumming School of Medicine, Department of Medical Genetics, and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada.
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38
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Chandler VK, Wares JP. RNA expression and disease tolerance are associated with a "keystone mutation" in the ochre sea star Pisaster ochraceus. PeerJ 2017; 5:e3696. [PMID: 28828278 PMCID: PMC5562136 DOI: 10.7717/peerj.3696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/26/2017] [Indexed: 11/20/2022] Open
Abstract
An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to "sea star wasting disease", a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
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Affiliation(s)
- V. Katelyn Chandler
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - John P. Wares
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Odum School of Ecology, University of Georgia, Athens, GA, United States of America
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39
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Scimone C, Donato L, Esposito T, Rinaldi C, D'Angelo R, Sidoti A. A novel RLBP1 gene geographical area-related mutation present in a young patient with retinitis punctata albescens. Hum Genomics 2017; 11:18. [PMID: 28764803 PMCID: PMC5540190 DOI: 10.1186/s40246-017-0114-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/25/2017] [Indexed: 11/10/2022] Open
Abstract
Background Autosomal recessive forms of retinitis punctata albescens (RPA) have been described. RPA is characterized by progressive retinal degeneration due to alteration in visual cycle and consequent deposit of photopigments in retinal pigment epithelium. Five loci have been linked to RPA onset. Among these, the retinaldehyde-binding protein 1 gene, RLBP1, is the most frequently involved and several founder mutations were reported. We report results of a genetic molecular investigation performed on a large Sicilian family in which appears a young woman with RPA. Results The proband is in homozygous condition for a novel RLBP1 single-pair deletion, and her healthy parents, both heterozygous, are not consanguineous. Thenovelc.398delC (p.P133Qfs*258) involves the exon 6 and leads to a premature stop codon, resulting in a truncated protein entirely missing of CRAL-TRIO lipid-binding domain. Pedigree analysis showed other non-consanguineous relatives heterozygous for the same mutation in the family. Extension of mutation research in the native town of the proband revealed its presence also in healthy subjects, in a heterozygous condition. Conclusions A novel RLBP1 truncating mutation was detected in a young girl affected by RPA. Although her parents are not consanguineous, the mutation was observed in a homozygous condition. Being them native of the same small Sicilian town of Fiumedinisi, the hypothesis of a geographical area-related mutation was assessed and confirmed.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Molecular Genetics and Preventive Medicine, University of Messina, via C. Valeria 1, I-98125, Messina, Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Neuroscience-applied Molecular Genetics and Predictive Medicine, I. E. ME. S. T, via Michele Miraglia 20, I-90139, Palermo, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Molecular Genetics and Preventive Medicine, University of Messina, via C. Valeria 1, I-98125, Messina, Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Neuroscience-applied Molecular Genetics and Predictive Medicine, I. E. ME. S. T, via Michele Miraglia 20, I-90139, Palermo, Italy
| | - Teresa Esposito
- Department of Experimental Medicine, Division of Human Physiology and Integrate Biological Functions "F. Bottazzi", University of Campania Luigi Vanvitelli, ex II University of Naples, via Santa Maria di Costantinipoli 16, I-80138, Naples, Italy
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Molecular Genetics and Preventive Medicine, University of Messina, via C. Valeria 1, I-98125, Messina, Italy.
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Molecular Genetics and Preventive Medicine, University of Messina, via C. Valeria 1, I-98125, Messina, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Molecular Genetics and Preventive Medicine, University of Messina, via C. Valeria 1, I-98125, Messina, Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Neuroscience-applied Molecular Genetics and Predictive Medicine, I. E. ME. S. T, via Michele Miraglia 20, I-90139, Palermo, Italy
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40
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A novel recessive TTN founder variant is a common cause of distal myopathy in the Serbian population. Eur J Hum Genet 2017; 25:572-581. [PMID: 28295036 DOI: 10.1038/ejhg.2017.16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/11/2017] [Accepted: 01/22/2017] [Indexed: 12/16/2022] Open
Abstract
Variants in the TTN gene have been associated with distal myopathies and other distinctive phenotypes involving skeletal and cardiac muscle. Through whole-exome sequencing we identified a novel stop-gain variant (c.107635C>T, p.(Gln35879Ter)) in the TTN gene, coding a part of the M-line of titin, in 14 patients with autosomal recessive distal myopathy and Serbian ancestry. All patients share a common 1 Mb core haplotype associated with c.107635C>T, suggesting a founder variant. In compound heterozygotes, nine other TTN variants were identified: four stop-gain, three frameshift, one missense and one splice donor variant. Patients homozygous for the common variant did not show significant clinical differences to the compound heterozygous patients. The clinical presentation of all patients was an adult onset distal myopathy with predominant lower limb involvement. In addition, most patients had normal to mildly elevated serum creatine kinase levels, myopathic electromyograms, normal cardiologic and respiratory tests and muscle pathology consistent with a dystrophic process. In this study, we describe a distinct phenotype for patients with distal myopathy associated with novel recessive TTN variants including a Serbian founder variant. Our results expand the phenotypic and genetic spectrum of titinopathies and will facilitate the diagnosis of this condition in patients of Serbian origin.
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41
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Identification and population history of CYP4V2 mutations in patients with Bietti crystalline corneoretinal dystrophy. Eur J Hum Genet 2017; 25:461-471. [PMID: 28051075 DOI: 10.1038/ejhg.2016.184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 11/15/2016] [Accepted: 11/24/2016] [Indexed: 11/08/2022] Open
Abstract
To identify known and novel CYP4V2 mutations in patients with Bietti crystalline cornea (BCD), expand the spectrum of CYP4V2 mutations, and characterize the population history of the c.802-8_810del17insGC mutation common in Asian populations, genomic DNA was isolated from peripheral blood samples from 58 unrelated patients with clinical diagnoses of BCD. Exons and flanking intronic regions of the CYP4V2 gene were dideoxy DNA sequenced. Nonpathogenic polymorphisms were excluded and known mutations were identified by sequencing 192 unaffected individuals from similar ethnic backgrounds and examination of online databases. The age of the c.802-8_810del17insGC mutation was estimated using three independent approaches. A total of 28 CYP4V2 mutations, 9 of which were novel, were detected in the 58 patients with BCD. These included 19 missense, 4 nonsense, 2 deletion, 2 splice site, and 1 insertion-deletion mutations. Two missense variants of uncertain significance were also detected. The age of the c.802-8_810del17insGC mutation was estimated to be 1040-8200 generations in the Chinese and 300-1100 generations in the Japanese populations. These results expand the mutation spectrum of CYP4V2, and provide insight into the origin of the c.802-8_810del17insGC mutation in the Chinese population and its transmission to the Japanese population.
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42
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Maksimova NR, Nogovicina AN, Kurtanov KA, Alekseeva EI. Population frequency and age of mutation G5741→A in gene NBAS which is a cause of SOPH syndrome in Sakha (Yakutia) Republic. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416090106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Gudbjartsson DF, Holm H, Sulem P, Masson G, Oddsson A, Magnusson OT, Saemundsdottir J, Helgadottir HT, Helgason H, Johannsdottir H, Gretarsdottir S, Gudjonsson SA, Njølstad I, Løchen ML, Baum L, Ma RCW, Sigfusson G, Kong A, Thorgeirsson G, Sverrisson JT, Thorsteinsdottir U, Stefansson K, Arnar DO. A frameshift deletion in the sarcomere gene MYL4 causes early-onset familial atrial fibrillation. Eur Heart J 2016; 38:27-34. [PMID: 27742809 DOI: 10.1093/eurheartj/ehw379] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 06/04/2016] [Accepted: 08/09/2016] [Indexed: 11/13/2022] Open
Abstract
AIMS Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia in man, causing substantial morbidity and mortality with a major worldwide public health impact. It is increasingly recognized as a highly heritable condition. This study aimed to determine genetic risk factors for early-onset AF. METHODS AND RESULTS We sequenced the whole genomes of 8453 Icelanders and imputed genotypes of the 25.5 million sequence variants we discovered into 1799 Icelanders with early-onset AF (diagnosed before 60 years of age) and 337 453 controls. Each sequence variant was tested for association based on multiplicative and recessive inheritance models. We discovered a rare frameshift deletion in the myosin MYL4 gene (c.234delC) that associates with early-onset AF under a recessive mode of inheritance (allelic frequency = 0.58%). We found eight homozygous carriers of the mutation, all of whom had early-onset AF. Six of the homozygotes were diagnosed by the age of 30 and the remaining two in their 50s. Three of the homozygotes had received pacemaker implantations due to sick sinus syndrome, three had suffered an ischemic stroke, and one suffered sudden cardiac death. CONCLUSIONS Through a population approach we found a loss of function mutation in the myosin gene MYL4 that, in the homozygous state, is completely penetrant for early-onset AF. The finding may provide novel mechanistic insight into the pathophysiology of this complex arrhythmia.
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Affiliation(s)
- Daniel F Gudbjartsson
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland .,School of Engineering and Natural Sciences, University of Iceland, Hjardarhaga 4, 107 Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland.,Department of Medicine, Landspitali- The National University Hospital, Hringbraut, 101 Reykjavik, Iceland
| | - Patrick Sulem
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland
| | - Gisli Masson
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Inger Njølstad
- Institute of Community Medicine, University of Tromsø, Postboks 6050, Langnes, 9037 Tromsø, Norway
| | - Maja-Lisa Løchen
- Institute of Community Medicine, University of Tromsø, Postboks 6050, Langnes, 9037 Tromsø, Norway.,Department of Cardiology, University Hospital of North Norway, Sykehusvegen 38, 9019 Tromsø, Norway
| | - Larry Baum
- School of Pharmacy, Chinese University of Hong Kong, Hong Kong
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Prince of Wales Hospital, 30 Ngan Shing Street, Sha Tin 999077 Hong Kong
| | - Gunnlaugur Sigfusson
- Children's Hospital, Landspitali- The National University Hospital, Hringbraut 101 Reykjavik, Iceland
| | - Augustine Kong
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Hjardarhaga 4, 107 Reykjavik, Iceland
| | - Guðmundur Thorgeirsson
- Department of Medicine, Landspitali- The National University Hospital, Hringbraut, 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
| | - Jon Th Sverrisson
- Department of Internal Medicine, Akureyri Hospital, Eyrarlandsvegur, 600 Akureyri, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
| | - David O Arnar
- deCODE genetics, Sturlugata 8, 101 Reykjavik, Iceland .,Department of Medicine, Landspitali- The National University Hospital, Hringbraut, 101 Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101 Reykjavik, Iceland
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44
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Apostolou P, Pertesi M, Aleporou-Marinou V, Dimitrakakis C, Papadimitriou C, Razis E, Christodoulou C, Fountzilas G, Yannoukakos D, Konstantopoulou I, Fostira F. Haplotype analysis reveals that the recurrent BRCA1 deletion of exons 23 and 24 is a Greek founder mutation. Clin Genet 2016; 91:482-487. [PMID: 27357818 DOI: 10.1111/cge.12824] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/07/2016] [Accepted: 06/24/2016] [Indexed: 11/28/2022]
Abstract
A recurrent large genomic rearrangement (LGR) encompassing exons 23 and 24 of the BRCA1 gene has been identified in breast-ovarian cancer families of Greek origin. Its breakpoints have been determined as c.5406 + 664_*8273del11052 (RefSeq: NM_007294.3) and a diagnostic polymerase chain reaction (PCR) has been set up for rapid screening. In a series of 2,092 high-risk families completely screened for BRCA1 and BRCA2 germline mutations, we have found the deletion in 35 families (1.68%), representing 7.83% of the mutations identified in both genes and 10.3% of the total BRCA1 mutations. In order to characterize this deletion as a founder mutation, haplotype analysis was conducted in 60 carriers from 35 families, using three BRCA1 intragenic microsatellite markers and four markers surrounding the BRCA1 locus. Our results demonstrate a common shared core disease-associated haplotype of 2.89Mb. Our calculations estimate that the deletion has originated from a common ancestor 1450 years ago, which most probably inhabited the Asia Minor area. The particular (LGR) is the third mutation of such type that is proven to have a Greek founder effect in the Greek population, illustrating the necessity for LGRs testing in individuals of Greek descent.
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Affiliation(s)
- P Apostolou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece.,Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - M Pertesi
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece.,Division of Hematology and Transfusion Medicine, Faculty of Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - V Aleporou-Marinou
- Department of Genetics & Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - C Dimitrakakis
- Breast Unit of the 1st Department of Obstetrics and Gynecology, Athens University Medical School, Athens, Greece
| | - C Papadimitriou
- Department of Clinical Therapeutics, "Alexandra" Hospital, School of Medicine, University of Athens, Athens, Greece
| | - E Razis
- Third Medical Oncology Department, Hygeia Hospital, Athens, Greece
| | - C Christodoulou
- Second Department of Medical Oncology, Metropolitan Hospital, Piraeus, Greece
| | - G Fountzilas
- School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - D Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - I Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
| | - F Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Athens, Greece
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Abdelhadi O, Iancu D, Tekman M, Stanescu H, Bockenhauer D, Kleta R. Founder mutation in KCNJ10 in Pakistani patients with EAST syndrome. Mol Genet Genomic Med 2016; 4:521-6. [PMID: 27652280 PMCID: PMC5023937 DOI: 10.1002/mgg3.227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/05/2016] [Accepted: 05/09/2016] [Indexed: 11/11/2022] Open
Abstract
Background EAST syndrome is an autosomal recessive disorder caused by loss‐of‐function mutations in the gene KCNJ10. Among the 14 pathogenic mutations described so far, the p.R65P mutation stands out as the most frequent one and is particularly associated with patients of Pakistani origin. As a result we aimed to establish the existence of a potential founder effect in the Pakistani population. Methods To this end, we genotyped 12 patients from seven families and we compared disease haplotypes with ethnically matched control chromosomes. This haplotype was used together with demographic data for Pakistan to estimate the age of this founder mutation. Results We identified a small homozygous 0.694 Mb region around the KCNJ10 p.R65P mutation that had identical haplotypes in all of the patients which were completely absent in the control sample. Based on current demographic data and knowledge about disease frequency, we estimate that this particular p.R65P mutation arose 20 generations (about 500 years) ago. Conclusion By knowing the prevalent mutation in a given population more efficient diagnostics can be performed and the families can benefit from specific counseling.
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Affiliation(s)
- Ola Abdelhadi
- Centre for Nephrology University College London London UK
| | - Daniela Iancu
- Centre for Nephrology University College London London UK
| | - Mehmet Tekman
- Centre for Nephrology University College London London UK
| | - Horia Stanescu
- Centre for Nephrology University College London London UK
| | | | - Robert Kleta
- Centre for Nephrology University College London London UK
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A Founder Effect for the HGD G360R Mutation in Italy: Implications for a Regional Screening of Alkaptonuria. JIMD Rep 2016. [PMID: 26960557 DOI: 10.1007/8904_2016_534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] Open
Abstract
We sought to establish rapid and specific genotyping methods for G360R mutation and for seven tightly linked markers in the homogentisate dioxygenase gene to address the question of whether G360R is a mutational hot spot or the result of a founder effect, as it has been repeatedly found in alkaptonuric patients from a geographic isolate in Italy.For G360R and single nucleotide polymorphism genotyping, high-resolution melting analysis was performed. Microsatellites were analysed by multiplex PCR and capillary electrophoresis. To investigate the natural history of the G360R mutation, we genotyped markers in 52 controls and in 8 unrelated patients from the UK and USA, who also segregated the G360R mutation, and calculated its age using DMLE+2.3 software.A distinct G360R-bearing haplotype was identified in all patients of Caucasian descent. Estimated mutation age was 545 generations (95% credible set, 402-854), suggesting that G360R arose in an ancestor who lived 8,000-10,000 years BC. Archaeological, historical and demographic data support that a G360R carrier has settled the remote valley where present-day population might have a heterozygote frequency of at least 6%.Given the late health-threatening complications of alkaptonuria and a cure within reach, inhabitants of this isolate would benefit from screening and genetic counselling.
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North TL, Ben-Shlomo Y, Cooper C, Deary IJ, Gallacher J, Kivimaki M, Kumari M, Martin RM, Pattie A, Sayer AA, Starr JM, Wong A, Kuh D, Rodriguez S, Day INM. A study of common Mendelian disease carriers across ageing British cohorts: meta-analyses reveal heterozygosity for alpha 1-antitrypsin deficiency increases respiratory capacity and height. J Med Genet 2016; 53:280-8. [PMID: 26831755 PMCID: PMC4819619 DOI: 10.1136/jmedgenet-2015-103342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/06/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Several recessive Mendelian disorders are common in Europeans, including cystic fibrosis (CFTR), medium-chain-acyl-Co-A-dehydrogenase deficiency (ACADM), phenylketonuria (PAH) and alpha 1-antitrypsin deficiency (SERPINA1). METHODS In a multicohort study of >19,000 older individuals, we investigated the relevant phenotypes in heterozygotes for these genes: lung function (forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC)) for CFTR and SERPINA1; cognitive measures for ACADM and PAH; and physical capability for ACADM, PAH and SERPINA1. RESULTS Findings were mostly negative but lung function in SERPINA1 (protease inhibitor (PI) Z allele, rs28929474) showed enhanced FEV1 and FVC (0.13 z-score increase in FEV1 (p=1.7 × 10(-5)) and 0.16 z-score increase in FVC (p=5.2 × 10(-8))) in PI-MZ individuals. Height adjustment (a known, strong correlate of FEV1 and FVC) revealed strong positive height associations of the Z allele (1.50 cm increase in height (p=3.6 × 10(-10))). CONCLUSIONS The PI-MZ rare (2%) SNP effect is nearly four times greater than the 'top' common height SNP in HMGA2. However, height only partially attenuates the SERPINA1-FEV1 or FVC association (around 50%) and vice versa. Height SNP variants have recently been shown to be positively selected collectively in North versus South Europeans, while the Z allele high frequency is localised to North Europe. Although PI-ZZ is clinically disadvantageous to lung function, PI-MZ increases both height and respiratory function; potentially a balanced polymorphism. Partial blockade of PI could conceivably form part of a future poly-therapeutic approach in very short children. The notion that elastase inhibition should benefit patients with chronic obstructive pulmonary disease may also merit re-evaluation. PI is already a therapeutic target: our findings invite a reconsideration of the optimum level in respiratory care and novel pathway potential for development of agents for the management of growth disorders.
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Affiliation(s)
- Teri-Louise North
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Yoav Ben-Shlomo
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK National Institute for Health Research Nutrition Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK National Institute for Health Research Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, UK Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - John Gallacher
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, UCL, London, UK
| | - Meena Kumari
- Department of Epidemiology and Public Health, UCL, London, UK ISER, University of Essex, Essex, UK
| | - Richard M Martin
- School of Social and Community Medicine, University of Bristol, Bristol, UK University of Bristol/University Hospitals Bristol NHS Foundation Trust National Institute for Health Research Bristol Nutrition Biomedical Research Unit, University of Bristol, Bristol, UK
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Avan Aihie Sayer
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Santiago Rodriguez
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ian N M Day
- School of Social and Community Medicine, University of Bristol, Bristol, UK
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Quint A, Sagi M, Carmi S, Daum H, Macarov M, Ben Neriah Z, Meiner V, Elpeleg O, Lerer I. An Ashkenazi founder mutation in the PKHD1 gene. Eur J Med Genet 2015; 59:86-90. [PMID: 26721323 DOI: 10.1016/j.ejmg.2015.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 12/11/2015] [Accepted: 12/21/2015] [Indexed: 11/29/2022]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is usually detected late in pregnancies in embryos with large echogenic kidneys accompanied by oligohydramnios. Hundreds of private pathogenic variants have been identified in the large PKHD1 gene in various populations. Yet, because of the large size of the gene, segregation analysis of microsatellite polymorphic markers residing in the PKDH1 locus has commonly been utilized for prenatal diagnosis. Keeping in mind the limitations of this strategy, we utilized it for testing 7 families with affected fetuses or newborns, of which in 5 at least one parent was Ashkenazi, and identified that the same haplotype was shared by the majority of the Ashkenazi parents (7/9). This led us to suspect that they carry the same founder mutation. Whole Exome analysis of DNA from a fetus of one of the families detected an already known pathogenic variant c.3761_3762delCCinsG, an indel variant resulting in frameshift (p.Ala1254GlyfsX49). This variant was detected in 9 parents (5 families), of them 7 individuals were Ashkenazi and one Moroccan Jew who shared the same haplotype, and one Ashkenazi, who carried the same variant on a recombinant haplotype. Screening for this variant in 364 Ashkenazi individuals detected 2 carriers. These findings suggest that although c.3761_3762delCCinsG is considered one of the frequent variants detected in unrelated individuals, and was thought to have occurred independently on various haplotypes, it is in fact a founder mutation in the Ashkenazi population.
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Affiliation(s)
- Adina Quint
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Israel
| | - Hagit Daum
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Macarov
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ziva Ben Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiela Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Orly Elpeleg
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Israela Lerer
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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50
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Choi JH, Balasubramanian R, Lee PH, Shaw ND, Hall JE, Plummer L, Buck CL, Kottler ML, Jarzabek K, Wołczynski S, Quinton R, Latronico AC, Dode C, Ogata T, Kim HG, Layman LC, Gusella JF, Crowley WF. Expanding the Spectrum of Founder Mutations Causing Isolated Gonadotropin-Releasing Hormone Deficiency. J Clin Endocrinol Metab 2015; 100. [PMID: 26207952 PMCID: PMC4596034 DOI: 10.1210/jc.2015-2262] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Loss of function (LoF) mutations in more than 20 genes are now known to cause isolated GnRH deficiency (IGD) in humans. Most causal IGD mutations are typically private, ie, limited to a single individual/pedigree. However, somewhat paradoxically, four IGD genes (GNRH1, TAC3, PROKR2, and GNRHR) have been shown to harbor LoF founder mutations that are shared by multiple unrelated individuals. It is not known whether similar founder mutations occur in other IGD genes. OBJECTIVE The objective of the study was to determine whether shared deleterious mutations in IGD-associated genes represent founder alleles. SETTING This study was an international collaboration among academic medical centers. METHODS IGD patients with shared mutations, defined as those documented in three or more unrelated probands in 14 IGD-associated genes, were identified from various academic institutions, the Human Gene Mutation Database, and literature reports by other international investigators. Haplotypes of single-nucleotide polymorphisms and short tandem repeats surrounding the mutations were constructed to assess genetic ancestry. RESULTS A total of eight founder mutations in five genes, GNRHR (Q106R, R262Q, R139H), TACR3 (W275X), PROKR2 (R85H), FGFR1 (R250Q, G687R), and HS6ST1 (R382W) were identified. Most founder alleles were present at low frequency in the general population. The estimated age of these mutant alleles ranged from 1925 to 5600 years and corresponded to the time of rapid human population expansion. CONCLUSIONS We have expanded the spectrum of founder alleles associated with IGD to a total of eight founder mutations. In contrast to the approximately 9000-year-old PROKR2 founder allele that may confer a heterozygote advantage, the rest of the founder alleles are relatively more recent in origin, in keeping with the timing of recent human population expansion and any selective heterozygote advantage of these alleles requires further evaluation.
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Affiliation(s)
- Jin-Ho Choi
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Ravikumar Balasubramanian
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Phil H Lee
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Natalie D Shaw
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Janet E Hall
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Lacey Plummer
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Cassandra L Buck
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Marie-Laure Kottler
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Katarzyna Jarzabek
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Sławomir Wołczynski
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Richard Quinton
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Ana Claudia Latronico
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Catherine Dode
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Tsutomu Ogata
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Hyung-Goo Kim
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Lawrence C Layman
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - James F Gusella
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - William F Crowley
- Harvard Reproductive Endocrine Sciences Center and Reproductive Endocrine Unit (J.-H.C., R.B., N.D.S., J.E.H., L.P., C.L.B., W.F.C.), and Department of Medicine, Psychiatric, and Neurodevelopmental Genetics Unit (P.H.L.), Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, and Center for Human Genetic Research (J.F.G.), Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts Boston, Massachusetts 02114; Department of Genetics (M.-L.K.), University Hospital, Caen, 14003, Caen Cedex, France; Department of Biology and Pathology of Human Reproduction in Bialystok (K.J.), Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, and Department of Reproduction and Gynecological Endocrinology (S.W.), Medical University of Bialystok, Sklodowskiej 24A, 15-276 Bialystok, Poland; Institute for Genetic Medicine (R.Q.), Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, United Kingdom; Disciplina de Endocrinologia (A.C.L.), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, 05403-900 Sao Paulo, Brazil; Laboratoire de Biochimie et Génétique Moléculaire (C.D.), Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université Paris-Descartes, 75014 Paris, France; Departments of Molecular Endocrinology and Pediatrics (T.O.), Hamamatsu University of School of Medicine, Hamamatsu 431-3192, Japan; Section of Reproductive Endocrinology, Infertility, and Genetics (H.-G.K., L.C.L.), Departments of Obstetrics and Gynecology and Neuroscience and Regenerative Medicine, Medical College of Georgia at Georgia Regents University, Augusta, Georgia 30912; and Department of Pediatrics (J.-H.C.), Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
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