1
|
Halvorsen M, de Schipper E, Boberg J, Strom N, Hagen K, Lindblad-Toh K, Karlsson E, Pedersen N, Bulik C, Fundín B, Landén M, Kvale G, Hansen B, Haavik J, Mattheisen M, Rück C, Mataix-Cols D, Crowley J. A Burden of Rare Copy Number Variants in Obsessive-Compulsive Disorder. RESEARCH SQUARE 2024:rs.3.rs-3749504. [PMID: 38260575 PMCID: PMC10802697 DOI: 10.21203/rs.3.rs-3749504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Current genetic research on obsessive-compulsive disorder (OCD) supports contributions to risk specifically from common single nucleotide variants (SNVs), along with rare coding SNVs and small insertion-deletions (indels). The contribution to OCD risk from large, rare copy number variants (CNVs), however, has not been formally assessed at a similar scale. Here we describe an analysis of rare CNVs called from genotype array data in 2,248 deeply phenotyped OCD cases and 3,608 unaffected controls from Sweden and Norway. We found that in general cases carry an elevated burden of large (>30kb, at least 15 probes) CNVs (OR=1.12, P=1.77×10-3). The excess rate of these CNVs in cases versus controls was around 0.07 (95% CI 0.02-0.11, P=2.58×10-3). This signal was largely driven by CNVs overlapping protein-coding regions (OR=1.19, P=3.08×10-4), particularly deletions impacting loss-of-function intolerant genes (pLI>0.995, OR=4.12, P=2.54×10-5). We did not identify any specific locus where CNV burden was associated with OCD case status at genome-wide significance, but we noted non-random recurrence of CNV deletions in cases (permutation P = 2.60×10-3). In cases where sufficient clinical data were available (n=1612) we found that carriers of neurodevelopmental duplications were more likely to have comorbid autism (P<0.001), and that carriers of deletions overlapping neurodevelopmental genes had lower treatment response (P=0.02). The results demonstrate a contribution of large, rare CNVs to OCD risk, and suggest that studies of rare coding variation in OCD would have increased power to identify risk genes if this class of variation were incorporated into formal tests.
Collapse
|
2
|
Ben-Mahmoud A, Kishikawa S, Gupta V, Leach NT, Shen Y, Moldovan O, Goel H, Hopper B, Ranguin K, Gruchy N, Maas SM, Lacassie Y, Kim SH, Kim WY, Quade BJ, Morton CC, Kim CH, Layman LC, Kim HG. A cryptic microdeletion del(12)(p11.21p11.23) within an unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome. Sci Rep 2023; 13:12984. [PMID: 37563198 PMCID: PMC10415337 DOI: 10.1038/s41598-023-40037-4] [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: 02/10/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
In a patient diagnosed with both Kallmann syndrome (KS) and intellectual disability (ID), who carried an apparently balanced translocation t(7;12)(q22;q24)dn, array comparative genomic hybridization (aCGH) disclosed a cryptic heterozygous 4.7 Mb deletion del(12)(p11.21p11.23), unrelated to the translocation breakpoint. This novel discovery prompted us to consider the possibility that the combination of KS and neurological disorder in this patient could be attributed to gene(s) within this specific deletion at 12p11.21-12p11.23, rather than disrupted or dysregulated genes at the translocation breakpoints. To further support this hypothesis, we expanded our study by screening five candidate genes at both breakpoints of the chromosomal translocation in a cohort of 48 KS patients. However, no mutations were found, thus reinforcing our supposition. In order to delve deeper into the characterization of the 12p11.21-12p11.23 region, we enlisted six additional patients with small copy number variations (CNVs) and analyzed eight individuals carrying small CNVs in this region from the DECIPHER database. Our investigation utilized a combination of complementary approaches. Firstly, we conducted a comprehensive phenotypic-genotypic comparison of reported CNV cases. Additionally, we reviewed knockout animal models that exhibit phenotypic similarities to human conditions. Moreover, we analyzed reported variants in candidate genes and explored their association with corresponding phenotypes. Lastly, we examined the interacting genes associated with these phenotypes to gain further insights. As a result, we identified a dozen candidate genes: TSPAN11 as a potential KS candidate gene, TM7SF3, STK38L, ARNTL2, ERGIC2, TMTC1, DENND5B, and ETFBKMT as candidate genes for the neurodevelopmental disorder, and INTS13, REP15, PPFIBP1, and FAR2 as candidate genes for KS with ID. Notably, the high-level expression pattern of these genes in relevant human tissues further supported their candidacy. Based on our findings, we propose that dosage alterations of these candidate genes may contribute to sexual and/or cognitive impairments observed in patients with KS and/or ID. However, the confirmation of their causal roles necessitates further identification of point mutations in these candidate genes through next-generation sequencing.
Collapse
Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Shotaro Kishikawa
- Gene Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Natalia T Leach
- Integrated Genetics, Laboratory Corporation of America Holdings, 3400 Computer Drive, Westborough, MA, 01581, USA
| | - Yiping Shen
- Division of Genetics and Genomics at Boston Children's Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Oana Moldovan
- Medical Genetics Service, Pediatric Department, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Himanshu Goel
- Hunter Genetics, Waratah, NSW, 2298, Australia
- University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Bruce Hopper
- Forster Genetics-Hunter New England Local Health District, Forster, NSW, 2428, Australia
| | - Kara Ranguin
- Department of Genetics, Reference Center for Rare Diseases of Developmental anomalies and polymalformative syndrome, CHU de Caen Normandie, Caen, France
| | - Nicolas Gruchy
- Department of Genetics, Reference Center for Rare Diseases of Developmental anomalies and polymalformative syndrome, CHU de Caen Normandie, Caen, France
| | - Saskia M Maas
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Reproduction and Development Research Institute, University of Amsterdam, Amsterdam, the Netherlands
| | - Yves Lacassie
- Division of Genetics, Department of Pediatrics, Louisiana State University, New Orleans, LA, 70118, USA
| | - Soo-Hyun Kim
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Bradley J Quade
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cynthia C Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, UK
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, USA
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, USA
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| |
Collapse
|
3
|
Ben-Mahmoud A, Kishikawa S, Gupta V, Leach NT, Shen Y, Moldovan O, Goel H, Hopper B, Ranguin K, Gruchy N, Maas SM, Lacassie Y, Kim SH, Kim WY, Quade BJ, Morton CC, Kim CH, Layman LC, Kim HG. A microdeletion del(12)(p11.21p11.23) with a cryptic unbalanced translocation t(7;12)(q21.13;q23.1) implicates new candidate loci for intellectual disability and Kallmann syndrome. RESEARCH SQUARE 2023:rs.3.rs-2572736. [PMID: 37034680 PMCID: PMC10081357 DOI: 10.21203/rs.3.rs-2572736/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
In an apparently balanced translocation t(7;12)(q22;q24)dn exhibiting both Kallmann syndrome (KS) and intellectual disability (ID), we detected a cryptic heterozygous 4.7 Mb del(12)(p11.21p11.23) unrelated to the translocation breakpoint. This new finding raised the possibility that KS combined with neurological disorder in this patient could be caused by gene(s) within this deletion at 12p11.21-12p11.23 instead of disrupted or dysregulated genes at the genomic breakpoints. Screening of five candidate genes at both breakpoints in 48 KS patients we recruited found no mutation, corroborating our supposition. To substantiate this hypothesis further, we recruited six additional subjects with small CNVs and analyzed eight individuals carrying small CNVs in this region from DECIPHER to dissect 12p11.21-12p11.23. We used multiple complementary approaches including a phenotypic-genotypic comparison of reported cases, a review of knockout animal models recapitulating the human phenotypes, and analyses of reported variants in the interacting genes with corresponding phenotypes. The results identified one potential KS candidate gene ( TSPAN11 ), seven candidate genes for the neurodevelopmental disorder ( TM7SF3 , STK38L , ARNTL2 , ERGIC2 , TMTC1 , DENND5B , and ETFBKMT ), and four candidate genes for KS with ID ( INTS13 , REP15 , PPFIBP1 , and FAR2 ). The high-level expression pattern in the relevant human tissues further suggested the candidacy of these genes. We propose that the dosage alterations of the candidate genes may contribute to sexual and/or cognitive impairment in patients with KS and/or ID. Further identification of point mutations through next generation sequencing will be necessary to confirm their causal roles.
Collapse
Affiliation(s)
| | | | | | | | | | - Oana Moldovan
- Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte
| | | | - Bruce Hopper
- Forster Genetics-Hunter New England Local Health District
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Functional analysis of structural variants in single cells using Strand-seq. Nat Biotechnol 2022:10.1038/s41587-022-01551-4. [PMID: 36424487 DOI: 10.1038/s41587-022-01551-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
Collapse
Affiliation(s)
- Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Kerstin K Rauwolf
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Roider
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | | | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sophie A Herbst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Ashley D Sanders
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany. .,Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
5
|
A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies. Sci Rep 2022; 12:4684. [PMID: 35304543 PMCID: PMC8933453 DOI: 10.1038/s41598-022-08663-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
Collapse
|
6
|
Liu S, Zeng Y, Wang C, Zhang Q, Chen M, Wang X, Wang L, Lu Y, Guo H, Bu F. seGMM: A New Tool for Gender Determination From Massively Parallel Sequencing Data. Front Genet 2022; 13:850804. [PMID: 35309142 PMCID: PMC8930203 DOI: 10.3389/fgene.2022.850804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
In clinical genetic testing, checking the concordance between self-reported gender and genotype-inferred gender from genomic data is a significant quality control measure because mismatched gender due to sex chromosomal abnormalities or misregistration of clinical information can significantly affect molecular diagnosis and treatment decisions. Targeted gene sequencing (TGS) is widely recommended as a first-tier diagnostic step in clinical genetic testing. However, the existing gender-inference tools are optimized for whole genome and whole exome data and are not adequate and accurate for analyzing TGS data. In this study, we validated a new gender-inference tool, seGMM, which uses unsupervised clustering (Gaussian mixture model) to determine the gender of a sample. The seGMM tool can also identify sex chromosomal abnormalities in samples by aligning the sequencing reads from the genotype data. The seGMM tool consistently demonstrated >99% gender-inference accuracy in a publicly available 1,000-gene panel dataset from the 1,000 Genomes project, an in-house 785 hearing loss gene panel dataset of 16,387 samples, and a 187 autism risk gene panel dataset from the Autism Clinical and Genetic Resources in China (ACGC) database. The performance and accuracy of seGMM was significantly higher for the targeted gene sequencing (TGS), whole exome sequencing (WES), and whole genome sequencing (WGS) datasets compared to the other existing gender-inference tools such as PLINK, seXY, and XYalign. The results of seGMM were confirmed by the short tandem repeat analysis of the sex chromosome marker gene, amelogenin. Furthermore, our data showed that seGMM accurately identified sex chromosomal abnormalities in the samples. In conclusion, the seGMM tool shows great potential in clinical genetics by determining the sex chromosomal karyotypes of samples from massively parallel sequencing data with high accuracy.
Collapse
Affiliation(s)
- Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Yuanyuan Zeng
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chao Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Qian Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Meilin Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaolu Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Lanchen Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Yu Lu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Yu Lu, ; Hui Guo, ; Fengxiao Bu,
| | - Hui Guo
- Center for Medical Genetics and Hunan Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- *Correspondence: Yu Lu, ; Hui Guo, ; Fengxiao Bu,
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Yu Lu, ; Hui Guo, ; Fengxiao Bu,
| |
Collapse
|
7
|
Smith G, Mathews D, Sander-Effron S, Requesens D, Turan N, Scheinfeldt L. Microsatellite Markers in Biobanking: A New Multiplexed Assay. Biopreserv Biobank 2021; 19:438-443. [PMID: 34468209 PMCID: PMC8665806 DOI: 10.1089/bio.2021.0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microsatellites, or MSATs, offer a fast and cost-effective way for biobanks to establish a biospecimen genetic profile. Importantly, this genetic profile can be used to authenticate multiple submissions derived from the same individual as well as biospecimens derived from the same original sample submission over time. While the Certificate of Confidentiality provided by the National Institutes of Health offers some meaningful protection to prevent the disclosure of potentially identifiable information to entities within the United States, we consider, in this study, the potential to offer additional protection to participants who choose to donate to biobanks by minimizing the use of forensic Combined DNA Index System (CODIS) MSAT markers in biobanking. To this end, we report the design and validation of a new multiplexed MSAT assay that does not include CODIS markers for use in biobanking operations and quality control management.
Collapse
Affiliation(s)
- Gretchen Smith
- Coriell Institute for Medical Research, Camden, New Jersey, USA
| | - Debra Mathews
- Berman Institute of Bioethics, Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Deborah Requesens
- Coriell Institute for Medical Research, Camden, New Jersey, USA.,The Orphan Disease Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nahid Turan
- Coriell Institute for Medical Research, Camden, New Jersey, USA
| | | |
Collapse
|
8
|
Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Rep 2020; 33:108474. [PMID: 33296649 DOI: 10.1016/j.celrep.2020.108474] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/25/2020] [Accepted: 11/12/2020] [Indexed: 01/03/2023] Open
Abstract
Bi-species, fusion-mediated, somatic cell reprogramming allows precise, organism-specific tracking of unknown lineage drivers. The fusion of Tcf7l1-/- murine embryonic stem cells with EBV-transformed human B cell lymphocytes, leads to the generation of bi-species heterokaryons. Human mRNA transcript profiling at multiple time points permits the tracking of the reprogramming of B cell nuclei to a multipotent state. Interrogation of a human B cell regulatory network with gene expression signatures identifies 8 candidate master regulator proteins. Of these 8 candidates, ectopic expression of BAZ2B, from the bromodomain family, efficiently reprograms hematopoietic committed progenitors into a multipotent state and significantly enhances their long-term clonogenicity, stemness, and engraftment in immunocompromised mice. Unbiased systems biology approaches let us identify the early driving events of human B cell reprogramming.
Collapse
Affiliation(s)
- Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentina Schiavone
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lukas Vlahos
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiaochuan Tu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Jordan Kesner
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Neus Romo
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Prem Subramaniam
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Jeremy Worley
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, J.P. Sulzberger Columbia Genome Center, Department of Biomedical Informatics, Department of Biochemistry and Molecular Biophysics, Department of Medicine, Columbia University, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| |
Collapse
|
9
|
Papp E, Hallberg D, Konecny GE, Bruhm DC, Adleff V, Noë M, Kagiampakis I, Palsgrove D, Conklin D, Kinose Y, White JR, Press MF, Drapkin R, Easwaran H, Baylin SB, Slamon D, Velculescu VE, Scharpf RB. Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines. Cell Rep 2019; 25:2617-2633. [PMID: 30485824 PMCID: PMC6481945 DOI: 10.1016/j.celrep.2018.10.096] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/07/2018] [Accepted: 10/25/2018] [Indexed: 12/27/2022] Open
Abstract
To improve our understanding of ovarian cancer, we performed genome-wide analyses of 45 ovarian cancer cell lines. Given the challenges of genomic analyses of tumors without matched normal samples, we developed approaches for detection of somatic sequence and structural changes and integrated these with epigenetic and expression alterations. Alterations not previously implicated in ovarian cancer included amplification or overexpression of ASXL1 and H3F3B, deletion or underexpression of CDC73 and TGF-beta receptor pathway members, and rearrangements of YAP1-MAML2 and IKZF2-ERBB4. Dose-response analyses to targeted therapies revealed unique molecular dependencies, including increased sensitivity of tumors with PIK3CA and PPP2R1A alterations to PI3K inhibitor GNE-493, MYC amplifications to PARP inhibitor BMN673, and SMAD3/4 alterations to MEK inhibitor MEK162. Genome-wide rearrangements provided an improved measure of sensitivity to PARP inhibition. This study provides a comprehensive and broadly accessible resource of molecular information for the development of therapeutic avenues in ovarian cancer. The overall survival of patients with late-stage ovarian cancer is dismal. To identify therapeutic opportunities, Papp et al. integrate genomic, epigenomic, and expression analyses to provide a resource of molecular abnormalities in ovarian cancer cell lines and use these to identify tumors sensitive to PARP, MEK, and PI3K inhibitors.
Collapse
Affiliation(s)
- Eniko Papp
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dorothy Hallberg
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gottfried E Konecny
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michaël Noë
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ioannis Kagiampakis
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doreen Palsgrove
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dylan Conklin
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Yasuto Kinose
- Department of Obstetrics and Gynecology Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael F Press
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology Penn Ovarian Cancer Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dennis Slamon
- Division of Hematology and Oncology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90024, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
10
|
Liang D, McHugh KM, Brophy PD, Shaikh N, Manak JR, Andrews P, Hakker I, Wang Z, Schwaderer AL, Hains DS. DNA copy number variations in children with vesicoureteral reflux and urinary tract infections. PLoS One 2019; 14:e0220617. [PMID: 31404082 PMCID: PMC6690579 DOI: 10.1371/journal.pone.0220617] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 07/19/2019] [Indexed: 11/18/2022] Open
Abstract
Vesicoureteral reflux (VUR) is a complex, heritable disorder. Genome-wide linkage analyses of families affected by VUR have revealed multiple genomic loci linked to VUR. These loci normally harbor a number of genes whose biologically functional variant is yet to be identified. DNA copy number variations (CNVs) have not been extensively studied at high resolution in VUR patients. In this study, we performed array comparative genomic hybridization (aCGH) on a cohort of patients with a history of both VUR and urinary tract infection (UTI) with the objective of identifying genetic variations responsible for VUR and/or UTI susceptibility. UTI/VUR-associated CNVs were identified by aCGH results from the 192 Randomized Intervention for Children With Vesicoureteral Reflux (RIVUR) patients compared to 683 controls. Rare, large CNVs that are likely pathogenic and lead to VUR development were identified using stringent analysis criteria. Because UTI is a common affliction with multiple risk factors, we utilized standard analysis to identify potential disease-modifying CNVs that can contribute to UTI risk. Gene ontology analysis identified that CNVs in innate immunity and development genes were enriched in RIVUR patients. CNVs affecting innate immune genes may contribute to UTI susceptibility in VUR patients and may provide the first step in assisting clinical medicine in determining adverse outcome risk in children with VUR.
Collapse
Affiliation(s)
- Dong Liang
- Department of Pediatrics, Indiana University, Indianapolis, IN, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Kirk M. McHugh
- Division of Anatomy, The Ohio State University, Columbus, OH, United States of America
| | - Pat D. Brophy
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - J. Robert Manak
- Departments of Biology and Pediatrics, University of Iowa, Iowa City, IA, United States of America
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Inessa Hakker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Andrew L. Schwaderer
- Department of Pediatrics, Indiana University, Indianapolis, IN, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Riley Hospital for Children at Indiana University Health, Indianapolis, IN, United States of America
| | - David S. Hains
- Department of Pediatrics, Indiana University, Indianapolis, IN, United States of America
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Riley Hospital for Children at Indiana University Health, Indianapolis, IN, United States of America
| |
Collapse
|
11
|
Ohuchi H, Sato K, Habuta M, Fujita H, Bando T. Congenital eye anomalies: More mosaic than thought? Congenit Anom (Kyoto) 2019; 59:56-73. [PMID: 30039880 DOI: 10.1111/cga.12304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022]
Abstract
The eye is a sensory organ that primarily captures light and provides the sense of sight, as well as delivering non-visual light information involving biological rhythms and neurophysiological activities to the brain. Since the early 1990s, rapid advances in molecular biology have enabled the identification of developmental genes, genes responsible for human congenital diseases, and relevant genes of mutant animals with various anomalies. In this review, we first look at the development of the eye, and we highlight seminal reports regarding archetypal gene defects underlying three developmental ocular disorders in humans: (1) holoprosencephaly (HPE), with cyclopia being exhibited in the most severe cases; (2) microphthalmia, anophthalmia, and coloboma (MAC) phenotypes; and (3) anterior segment dysgenesis (ASDG), known as Peters anomaly and its related disorders. The recently developed methods, such as next-generation sequencing and genome editing techniques, have aided the discovery of gene mutations in congenital eye diseases and gene functions in normal eye development. Finally, we discuss Pax6-genome edited mosaic eyes and propose that somatic mosaicism in developmental gene mutations should be considered a causal factor for variable phenotypes, sporadic cases, and de novo mutations in human developmental disorders.
Collapse
Affiliation(s)
- Hideyo Ohuchi
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Keita Sato
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Munenori Habuta
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hirofumi Fujita
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tetsuya Bando
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| |
Collapse
|
12
|
Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research. Sci Rep 2019; 9:4889. [PMID: 30894562 PMCID: PMC6426863 DOI: 10.1038/s41598-019-40897-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Genotyped human B-lymphoblastoid cell lines (LCLs) are widely used models in mapping quantitative trait loci for chromatin features, gene expression, and drug response. The extent of genotype-independent functional genomic variability of the LCL model, although largely overlooked, may inform association study design. In this study, we use flow cytometry, chromatin immunoprecipitation sequencing and mRNA sequencing to study surface marker patterns, quantify genome-wide chromatin changes (H3K27ac) and transcriptome variability, respectively, among five isogenic LCLs derived from the same individual. Most of the studied LCLs were non-monoclonal and had mature B cell phenotypes. Strikingly, nearly one-fourth of active gene regulatory regions showed significantly variable H3K27ac levels, especially enhancers, among which several were classified as clustered enhancers. Large, contiguous genomic regions showed signs of coordinated activity change. Regulatory differences were mirrored by mRNA expression changes, preferentially affecting hundreds of genes involved in specialized cellular processes including immune and drug response pathways. Differential expression of DPYD, an enzyme involved in 5-fluorouracil (5-FU) catabolism, was associated with variable LCL growth inhibition mediated by 5-FU. The extent of genotype-independent functional genomic variability might highlight the need to revisit study design strategies for LCLs in pharmacogenomics.
Collapse
|
13
|
Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
Collapse
Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
| |
Collapse
|
14
|
Scheinfeldt LB, Hodges K, Pevsner J, Berlin D, Turan N, Gerry NP. Genetic and genomic stability across lymphoblastoid cell line expansions. BMC Res Notes 2018; 11:558. [PMID: 30075799 PMCID: PMC6076395 DOI: 10.1186/s13104-018-3664-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/30/2018] [Indexed: 11/21/2022] Open
Abstract
Objective Lymphoblastoid cell lines are widely used in genetic and genomic studies. Previous work has characterized variant stability in transformed culture and across culture passages. Our objective was to extend this work to evaluate single nucleotide polymorphism and structural variation across cell line expansions, which are commonly used in biorepository distribution. Our study used DNA and cell lines sampled from six research participants. We assayed genome-wide genetic variants and inferred structural variants for DNA extracted from blood, from transformed cell cultures, and from three generations of expansions. Results Single nucleotide variation was stable between DNA and expanded cell lines (ranging from 99.90 to 99.98% concordance). Structural variation was less consistent across expansions (median 33% concordance) with a noticeable decrease in later expansions. In summary, we demonstrate consistency between SNPs assayed from whole blood DNA and LCL DNA; however, more caution should be taken in using LCL DNA to study structural variation. Electronic supplementary material The online version of this article (10.1186/s13104-018-3664-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Laura B Scheinfeldt
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08003, USA.
| | - Kelly Hodges
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08003, USA
| | - Jonathan Pevsner
- Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Dorit Berlin
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08003, USA
| | - Nahid Turan
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08003, USA
| | - Norman P Gerry
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08003, USA.,Advanced BioMedical Laboratories, 1605 Industrial Hwy, Cinnaminson, NJ, 08007, USA
| |
Collapse
|
15
|
Viswanath B, Rao NP, Narayanaswamy JC, Sivakumar PT, Kandasamy A, Kesavan M, Mehta UM, Venkatasubramanian G, John JP, Mukherjee O, Purushottam M, Kannan R, Mehta B, Kandavel T, Binukumar B, Saini J, Jayarajan D, Shyamsundar A, Moirangthem S, Vijay Kumar KG, Thirthalli J, Chandra PS, Gangadhar BN, Murthy P, Panicker MM, Bhalla US, Chattarji S, Benegal V, Varghese M, Reddy JYC, Raghu P, Rao M, Jain S. Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science. BMC Psychiatry 2018; 18:106. [PMID: 29669557 PMCID: PMC5907468 DOI: 10.1186/s12888-018-1674-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND There is emerging evidence that there are shared genetic, environmental and developmental risk factors in psychiatry, that cut across traditional diagnostic boundaries. With this background, the Discovery biology of neuropsychiatric syndromes (DBNS) proposes to recruit patients from five different syndromes (schizophrenia, bipolar disorder, obsessive compulsive disorder, Alzheimer's dementia and substance use disorders), identify those with multiple affected relatives, and invite these families to participate in this study. The families will be assessed: 1) To compare neuro-endophenotype measures between patients, first degree relatives (FDR) and healthy controls., 2) To identify cellular phenotypes which differentiate the groups., 3) To examine the longitudinal course of neuro-endophenotype measures., 4) To identify measures which correlate with outcome, and 5) To create a unified digital database and biorepository. METHODS The identification of the index participants will occur at well-established specialty clinics. The selected individuals will have a strong family history (with at least another affected FDR) of mental illness. We will also recruit healthy controls without family history of such illness. All recruited individuals (N = 4500) will undergo brief clinical assessments and a blood sample will be drawn for isolation of DNA and peripheral blood mononuclear cells (PBMCs). From among this set, a subset of 1500 individuals (300 families and 300 controls) will be assessed on several additional assessments [detailed clinical assessments, endophenotype measures (neuroimaging- structural and functional, neuropsychology, psychophysics-electroencephalography, functional near infrared spectroscopy, eye movement tracking)], with the intention of conducting repeated measurements every alternate year. PBMCs from this set will be used to generate lymphoblastoid cell lines, and a subset of these would be converted to induced pluripotent stem cell lines and also undergo whole exome sequencing. DISCUSSION We hope to identify unique and overlapping brain endophenotypes for major psychiatric syndromes. In a proportion of subjects, we expect these neuro-endophenotypes to progress over time and to predict treatment outcome. Similarly, cellular assays could differentiate cell lines derived from such groups. The repository of biomaterials as well as digital datasets of clinical parameters, will serve as a valuable resource for the broader scientific community who wish to address research questions in the area.
Collapse
Affiliation(s)
- Biju Viswanath
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Naren P. Rao
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | | | | | - Arun Kandasamy
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Muralidharan Kesavan
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | | | | | - John P. John
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Odity Mukherjee
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bangalore, India
| | - Meera Purushottam
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Ramakrishnan Kannan
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Bhupesh Mehta
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Thennarasu Kandavel
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - B. Binukumar
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Jitender Saini
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Deepak Jayarajan
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - A. Shyamsundar
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Sydney Moirangthem
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - K. G. Vijay Kumar
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Jagadisha Thirthalli
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Prabha S. Chandra
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | | | - Pratima Murthy
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Mitradas M. Panicker
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bangalore, India
| | - Upinder S. Bhalla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bangalore, India
| | - Sumantra Chattarji
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bangalore, India
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bangalore, India
| | - Vivek Benegal
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Mathew Varghese
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | | | - Padinjat Raghu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR), Bangalore, India
| | - Mahendra Rao
- Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bangalore, India
| | - Sanjeev Jain
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| |
Collapse
|
16
|
Xu J, Peng X, Chen Y, Zhang Y, Ma Q, Liang L, Carter AC, Lu X, Wu CI. Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity. eLife 2017; 6. [PMID: 29251591 PMCID: PMC5734875 DOI: 10.7554/elife.28070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/28/2017] [Indexed: 01/06/2023] Open
Abstract
Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral uni-cellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~ 600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming ‘de-sexualized’. Surprisingly, the active X often doubled, accompanied by the addition of one haploid complement of autosomes, leading to an X:A ratio of 2:3 from the extant ratio of 1:2. Theoretical modeling of the frequency distribution of X:A karyotypes suggests that the 2:3 ratio confers a higher fitness and may reflect aspects of sex chromosome evolution. Multicellular life relies on a group of cells working together for a common interest. To study these cells, researchers take them out of the organism and grow them in the laboratory. Instead of growing as part of organs and tissues, the cells normally have a free-living lifestyle. Because multicellular life evolved from single-celled organisms, laboratory-grown cells can be considered as life forms that are evolving backward from a multicellular to a single-celled existence. Normally, the cells that make up most of the tissues in the human body have 22 pairs of chromosomes known as autosomes and a pair of sex chromosomes. The cells of women have two X sex chromosomes, one of which is inactive, while those of men have one X and one Y chromosome. However, free-living single cells do not need to distinguish between male and female cells. Xu, Peng, Chen et al. have now studied the chromosomes of cancer cells taken from over 600 people and grown in the laboratory. As the cells evolved in response to their free-living lifestyle, they became ‘de-sexualized’; male cells lost their Y chromosome, while female cells abandoned their inactive X chromosome. The cells then evolved toward a new state in which they possessed two active X chromosomes and three sets of autosomes. This new configuration suggests that the current X chromosome to autosome ratio may not be optimal for fitness and hence sheds some light on how mammalian sex chromosomes evolved. It is currently thought that as cancerous tumors grow, their cells evolve to favor their own interests over the common interests of the rest of the organism. In this way, they develop characteristics more like those of single cells. Further research is therefore needed to investigate whether changes occur to the chromosomes of cancer cells growing within the body, and whether this gives them an advantage over normal cells.
Collapse
Affiliation(s)
- Jin Xu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuezheng Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qin Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Liang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, United States
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
| |
Collapse
|
17
|
Dong Z, Wang H, Chen H, Jiang H, Yuan J, Yang Z, Wang WJ, Xu F, Guo X, Cao Y, Zhu Z, Geng C, Cheung WC, Kwok YK, Yang H, Leung TY, Morton CC, Cheung SW, Choy KW. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics. Genet Med 2017; 20:697-707. [PMID: 29095815 PMCID: PMC5932280 DOI: 10.1038/gim.2017.170] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/14/2017] [Indexed: 02/04/2023] Open
Abstract
Purpose Recent studies demonstrate that whole-genome sequencing (WGS) enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in The 1000 Genomes Project without knowing affected bands. Methods The 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparently BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories. We applied our analytical tool to 1,166 genomes from the 1000 Genomes Project with sufficient physical coverage (8.25-fold). Results Our approach detected four reciprocal balanced translocations and four inversions ranging in size from 57.9 kb to 13.3 Mb, all of which were confirmed by cytogenetic methods and PCR studies. One of DNAs has a subtle translocation that is not readily identified by chromosome analysis due to similar banding patterns and size of exchanged segments, and another results in disruption of all transcripts of an OMIM gene. Conclusions Our study demonstrates the extension of utilizing low-coverage WGS for unbiased detection of BCAs including translocations and inversions previously unknown in the 1000 Genomes Project.
Collapse
Affiliation(s)
- Zirui Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,BGI-Shenzhen, Shenzhen, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huilin Wang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research and Transformation Team, Shenzhen, China
| | - Haixiao Chen
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jianying Yuan
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhenjun Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenzhen Zhu
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Chunyu Geng
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Wan Chee Cheung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Harvard Medical School, Boston, Massachusetts, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA. .,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Center, Manchester, UK.
| | - Sau Wai Cheung
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China. .,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China.
| |
Collapse
|
18
|
Schork NJ, Nazor K. Integrated Genomic Medicine: A Paradigm for Rare Diseases and Beyond. ADVANCES IN GENETICS 2017; 97:81-113. [PMID: 28838357 PMCID: PMC6383766 DOI: 10.1016/bs.adgen.2017.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Individualized medicine, or the tailoring of therapeutic interventions to a patient's unique genetic, biochemical, physiological, exposure and behavioral profile, has been enhanced, if not enabled, by modern biomedical technologies such as high-throughput DNA sequencing platforms, induced pluripotent stem cell assays, biomarker discovery protocols, imaging modalities, and wireless monitoring devices. Despite successes in the isolated use of these technologies, however, it is arguable that their combined and integrated use in focused studies of individual patients is the best way to not only tailor interventions for those patients, but also shed light on treatment strategies for patients with similar conditions. This is particularly true for individuals with rare diseases since, by definition, they will require study without recourse to other individuals, or at least without recourse to many other individuals. Such integration and focus will require new biomedical scientific paradigms and infrastructure, including the creation of databases harboring study results, the formation of dedicated multidisciplinary research teams and new training programs. We consider the motivation and potential for such integration, point out areas in need of improvement, and argue for greater emphasis on improving patient health via technological innovations, not merely improving the technologies themselves. We also argue that the paradigm described can, in theory, be extended to the study of individuals with more common diseases.
Collapse
Affiliation(s)
- Nicholas J. Schork
- The Translational Genomics Research Institute, 445 North Fifth Street, Phoenix, AZ 85004, , 858-794-4054
| | - Kristopher Nazor
- MYi Diagnostics and Discovery, 5310 Eastgate Mall, San Diego, CA 92121, , 858-458-9305
| |
Collapse
|
19
|
Huang AY, Yu D, Davis LK, Sul JH, Tsetsos F, Ramensky V, Zelaya I, Ramos EM, Osiecki L, Chen JA, McGrath LM, Illmann C, Sandor P, Barr CL, Grados M, Singer HS, Nöthen MM, Hebebrand J, King RA, Dion Y, Rouleau G, Budman CL, Depienne C, Worbe Y, Hartmann A, Müller-Vahl KR, Stuhrmann M, Aschauer H, Stamenkovic M, Schloegelhofer M, Konstantinidis A, Lyon GJ, McMahon WM, Barta C, Tarnok Z, Nagy P, Batterson JR, Rizzo R, Cath DC, Wolanczyk T, Berlin C, Malaty IA, Okun MS, Woods DW, Rees E, Pato CN, Pato MT, Knowles JA, Posthuma D, Pauls DL, Cox NJ, Neale BM, Freimer NB, Paschou P, Mathews CA, Scharf JM, Coppola G. Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for Tourette Syndrome. Neuron 2017; 94:1101-1111.e7. [PMID: 28641109 PMCID: PMC5568251 DOI: 10.1016/j.neuron.2017.06.010] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/14/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022]
Abstract
Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2.28, 95% CI [1.39-3.79], p = 1.2 × 10-3) and known, pathogenic CNVs (OR = 3.03 [1.85-5.07], p = 1.5 × 10-5). We also identified two individual, genome-wide significant loci, each conferring a substantial increase in TS risk (NRXN1 deletions, OR = 20.3, 95% CI [2.6-156.2]; CNTN6 duplications, OR = 10.1, 95% CI [2.3-45.4]). Approximately 1% of TS cases carry one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS.
Collapse
Affiliation(s)
- Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fotis Tsetsos
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Vasily Ramensky
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Institusky 9, Moscow 141701, Russian Federation
| | - Ivette Zelaya
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eliana Marisa Ramos
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jason A Chen
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lauren M McGrath
- Department of Psychology, University of Denver, Denver, CO 80210, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Paul Sandor
- Toronto Western Research Institute, University Health Network and Youthdale Treatment Centres, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Marco Grados
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harvey S Singer
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany; Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Robert A King
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yves Dion
- University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Guy Rouleau
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC H3A 2B4, Canada
| | - Cathy L Budman
- Hofstra Northwell School of Medicine, Hempstead, NY 11549, USA
| | - Christel Depienne
- IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, 67404 Illkirch Cedex, France; Brain and Spine Institute, UPMC/INSERM UMR_S1127, 75013 Paris Cedex 05, France
| | - Yulia Worbe
- Brain and Spine Institute, UPMC/INSERM UMR_S1127, 75013 Paris Cedex 05, France
| | - Andreas Hartmann
- Brain and Spine Institute, UPMC/INSERM UMR_S1127, 75013 Paris Cedex 05, France
| | - Kirsten R Müller-Vahl
- Clinic of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, 30625 Hannover, Germany
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, 1090 Vienna, Austria; Biopsychosocial Corporation, 1090 Vienna, Austria
| | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, 1090 Vienna, Austria
| | - Monika Schloegelhofer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, 1090 Vienna, Austria
| | - Anastasios Konstantinidis
- Department of Psychiatry and Psychotherapy, Medical University Vienna, 1090 Vienna, Austria; Center for Mental Health Muldenstrasse, BBRZMed, 4020 Linz, Austria
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1085 Budapest, Hungary
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, 1021 Budapest, Hungary
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, 1021 Budapest, Hungary
| | | | - Renata Rizzo
- Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, 95131 Catania, Italy
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen & Drenthe Mental Health Center, 9700 RB Groningen, the Netherlands; Department of Clinical Psychology, Utrecht University, 3584 CS Utrecht, the Netherlands
| | - Tomasz Wolanczyk
- Department of Child Psychiatry, Medical University of Warsaw, 00-001 Warsaw, Poland
| | - Cheston Berlin
- Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Irene A Malaty
- Department of Neurology and Center for Movement Disorders and Neurorestoration, University of Florida, Gainesville, FL 32607, USA
| | - Michael S Okun
- Department of Neurology and Center for Movement Disorders and Neurorestoration, University of Florida, Gainesville, FL 32607, USA
| | - Douglas W Woods
- Marquette University, Milwaukee, WI 53233, USA; University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Elliott Rees
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff CF24 4HQ, Wales, UK
| | - Carlos N Pato
- SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | | | - James A Knowles
- Department of Psychiatry & Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - David L Pauls
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
20
|
Joesch-Cohen LM, Glusman G. Differences between the genomes of lymphoblastoid cell lines and blood-derived samples. ADVANCES IN GENOMICS AND GENETICS 2017; 7:1-9. [PMID: 28736497 PMCID: PMC5520659 DOI: 10.2147/agg.s128824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lymphoblastoid cell lines (LCLs) represent a convenient research tool for expanding the amount of biologic material available from an individual. LCLs are commonly used as reference materials, most notably from the Genome in a Bottle Consortium. However, the question remains how faithfully LCL-derived genome assemblies represent the germline genome of the donor individual as compared to the genome assemblies derived from peripheral blood mononuclear cells. We present an in-depth comparison of a large collection of LCL- and peripheral blood mononuclear cell-derived genomes in terms of distributions of coverage and copy number alterations. We found significant differences in the depth of coverage and copy number calls, which may be driven by differential replication timing. Importantly, these copy number changes preferentially affect regions closer to genes and with higher GC content. This suggests that genomic studies based on LCLs may display locus-specific biases, and that conclusions based on analysis of depth of coverage and copy number variation may require further scrutiny.
Collapse
|
21
|
Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
Collapse
|
22
|
Duan J, Sanders AR, Moy W, Drigalenko EI, Brown EC, Freda J, Leites C, Göring HHH, Gejman PV. Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants. Hum Mol Genet 2015; 24:4674-85. [PMID: 26022996 DOI: 10.1093/hmg/ddv199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/26/2015] [Indexed: 02/06/2023] Open
Abstract
We searched a gene expression dataset comprised of 634 schizophrenia (SZ) cases and 713 controls for expression outliers (i.e., extreme tails of the distribution of transcript expression values) with SZ cases overrepresented compared with controls. These outlier genes were enriched for brain expression and for genes known to be associated with neurodevelopmental disorders. SZ cases showed higher outlier burden (i.e., total outlier events per subject) than controls for genes within copy number variants (CNVs) associated with SZ or neurodevelopmental disorders. Outlier genes were enriched for CNVs and for rare putative regulatory variants, but this only explained a small proportion of the outlier subjects, highlighting the underlying presence of additional genetic and potentially, epigenetic mechanisms.
Collapse
Affiliation(s)
- Jubao Duan
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA,
| | - Alan R Sanders
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Winton Moy
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Eugene I Drigalenko
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | - Eric C Brown
- Center for Biomedical Research Informatics, NorthShore University HealthSystem, Evanston, IL, USA
| | | | | | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | | | - Pablo V Gejman
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| |
Collapse
|
23
|
Kember RL, Georgi B, Bailey-Wilson JE, Stambolian D, Paul SM, Bućan M. Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder. BMC Genet 2015; 16:27. [PMID: 25887117 PMCID: PMC4382929 DOI: 10.1186/s12863-015-0184-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Bipolar affective disorder (BP) is a common, highly heritable psychiatric disorder characterized by periods of depression and mania. Using dense SNP genotype data, we characterized CNVs in 388 members of an Old Order Amish Pedigree with bipolar disorder. We identified CNV regions arising from common ancestral mutations by utilizing the pedigree information. By combining this analysis with whole genome sequence data in the same individuals, we also explored the role of compound heterozygosity. RESULTS Here we describe 541 inherited CNV regions, of which 268 are rare in a control population of European origin but present in a large number of Amish individuals. In addition, we highlight a set of CNVs found at higher frequencies in BP individuals, and within genes known to play a role in human development and disease. As in prior reports, we find no evidence for an increased burden of CNVs in BP individuals, but we report a trend towards a higher burden of CNVs in known Mendelian disease loci in bipolar individuals (BPI and BPII, p = 0.06). CONCLUSIONS We conclude that CNVs may be contributing factors in the phenotypic presentation of mood disorders and co-morbid medical conditions in this family. These results reinforce the hypothesis of a complex genetic architecture underlying BP disorder, and suggest that the role of CNVs should continue to be investigated in BP data sets.
Collapse
Affiliation(s)
- Rachel L Kember
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Benjamin Georgi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Steven M Paul
- Appel Alzheimer's Disease Research Institute, Mind and Brain Institute, Weill Cornell Medical College, New York, NY, USA.
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
24
|
White PS, Xie HM, Werner P, Glessner J, Latney B, Hakonarson H, Goldmuntz E. Analysis of chromosomal structural variation in patients with congenital left-sided cardiac lesions. ACTA ACUST UNITED AC 2014; 100:951-64. [DOI: 10.1002/bdra.23279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter S. White
- The Center for Biomedical Informatics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
| | - Hongbo M. Xie
- The Center for Biomedical Informatics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Petra Werner
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Joseph Glessner
- The Center for Applied Genomics, Department of Pediatrics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Brande Latney
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Hakon Hakonarson
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
- The Center for Applied Genomics, Department of Pediatrics; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Elizabeth Goldmuntz
- Department of Pediatrics; Perelman School of Medicine, University of Pennsylvania; Philadelphia Pennsylvania
- The Division of Cardiology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| |
Collapse
|
25
|
Upregulation of TFAM and mitochondria copy number in human lymphoblastoid cells. Mitochondrion 2014; 15:52-8. [PMID: 24462998 DOI: 10.1016/j.mito.2014.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 01/10/2014] [Accepted: 01/15/2014] [Indexed: 12/12/2022]
Abstract
Mitochondria are central to several physiological and pathological conditions in humans. In the present study, we performed copy number analysis of nuclear encoded mitochondrial genes, in peripheral blood mononuclear cells (PBMCs) and its representative lymphoblastoid cells (LCLs). We have observed hyper diploid copies of mitochondrial transcription factor A (TFAM) gene in the LCLs along with increased mtDNA copy number, mitochondrial mass, intracellular ROS and mitochondrial membrane potential, suggesting elevated mitochondrial biogenesis in LCLs. Gene expression analysis confirmed TFAM over-expression in LCLs when compared to PBMC. Based on our observation, we suggest that increased copy number of TFAM gene upregulates its expression, increases mtDNA copy numbers and protects it from oxidative stress induced damage in the transformed LCLs.
Collapse
|
26
|
Bendjilali N, Hsueh WC, He Q, Willcox DC, Nievergelt CM, Donlon TA, Kwok PY, Suzuki M, Willcox BJ. Who are the Okinawans? Ancestry, genome diversity, and implications for the genetic study of human longevity from a geographically isolated population. J Gerontol A Biol Sci Med Sci 2014; 69:1474-84. [PMID: 24444611 DOI: 10.1093/gerona/glt203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome-more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans.
Collapse
Affiliation(s)
| | - Wen-Chi Hsueh
- Departments of Medicine and Epidemiology & Biostatistics, University of California, San Francisco
| | - Qimei He
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Department of Research, Kuakini Medical Center, Honolulu, Hawaii
| | | | | | - Timothy A Donlon
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Ohana Genetics, Honolulu, Hawaii
| | - Pui-Yan Kwok
- Department of Dermatology, Institute for Human Genetics, and Cardiovascular Research Institute, University of California, San Francisco
| | - Makoto Suzuki
- Okinawa Research Center for Longevity Science, Urasoe, Okinawa, Japan. Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Bradley J Willcox
- Pacific Health Research and Education Institute, Honolulu, Hawaii. Department of Research, Kuakini Medical Center, Honolulu, Hawaii. Okinawa Research Center for Longevity Science, Urasoe, Okinawa, Japan. Department of Geriatric Medicine, John A Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| |
Collapse
|
27
|
Concerns regarding "Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA". Genomics 2013; 102:430. [PMID: 23916999 DOI: 10.1016/j.ygeno.2013.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 07/26/2013] [Indexed: 11/22/2022]
|
28
|
Handel AE, Sandve GK, Disanto G, Berlanga-Taylor AJ, Gallone G, Hanwell H, Drabløs F, Giovannoni G, Ebers GC, Ramagopalan SV. Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. BMC Med 2013; 11:163. [PMID: 23849224 PMCID: PMC3710212 DOI: 10.1186/1741-7015-11-163] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 06/20/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated with autoimmune diseases. We aimed to investigate VDR binding in primary CD4+ cells from healthy volunteers. METHODS We extracted CD4+ cells from nine healthy volunteers. Each sample underwent VDR ChIP-seq. Our results were analyzed in relation to published ChIP-seq and RNA-seq data in the Genomic HyperBrowser. We used MEMEChIP for de novo motif discovery. 25-Hydroxyvitamin D levels were measured using liquid chromatography-tandem mass spectrometry and samples were divided into vitamin D sufficient (25(OH)D ≥75 nmol/L) and insufficient/deficient (25(OH)D <75 nmol/L) groups. RESULTS We found that the amount of VDR binding is correlated with the serum level of 25-hydroxyvitamin D (r = 0.92, P= 0.0005). In vivo VDR binding sites are enriched for autoimmune disease associated loci, especially when 25-hydroxyvitamin D levels (25(OH)D) were sufficient (25(OH)D ≥75: 3.13-fold, P<0.0001; 25(OH)D <75: 2.76-fold, P<0.0001; 25(OH)D ≥75 enrichment versus 25(OH)D <75 enrichment: P= 0.0002). VDR binding was also enriched near genes associated specifically with T-regulatory and T-helper cells in the 25(OH)D ≥75 group. MEME ChIP did not identify any VDR-like motifs underlying our VDR ChIP-seq peaks. CONCLUSION Our results show a direct correlation between in vivo 25-hydroxyvitamin D levels and the number of VDR binding sites, although our sample size is relatively small. Our study further implicates VDR binding as important in gene-environment interactions underlying the development of autoimmunity and provides a biological rationale for 25-hydroxyvitamin D sufficiency being based at 75 nmol/L. Our results also suggest that VDR binding in response to physiological levels of vitamin D occurs predominantly in a VDR motif-independent manner.
Collapse
Affiliation(s)
- Adam E Handel
- Medical Research Council Functional Genomics Unit and Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Baugher JD, Baugher BD, Shirley MD, Pevsner J. Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method. BMC Genomics 2013; 14:367. [PMID: 23724825 PMCID: PMC3680018 DOI: 10.1186/1471-2164-14-367] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/14/2013] [Indexed: 11/25/2022] Open
Abstract
Background Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism are largely unknown. Most mosaic alterations remain undetectable with current analytical approaches, although the presence of such alterations is increasingly implicated as causative for disease. Results Here, we present the Parent-of-Origin-based Detection (POD) method for chromosomal abnormality detection in trio-based SNP microarray data. Our software implementation, triPOD, was benchmarked using a simulated dataset, outperformed comparable software for sensitivity of abnormality detection, and displayed substantial improvement in the detection of low-level mosaicism while maintaining comparable specificity. Examples of low-level mosaic abnormalities from a large autism dataset demonstrate the benefits of the increased sensitivity provided by triPOD. The triPOD analyses showed robustness across multiple types of Illumina microarray chips. Two large, clinically-relevant datasets were characterized and compared. Conclusions Our method and software provide a significant advancement in the ability to detect low-level mosaic abnormalities, thereby opening new avenues for research into the implications of mosaicism in pathogenic and non-pathogenic processes.
Collapse
Affiliation(s)
- Joseph D Baugher
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | | | | |
Collapse
|