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Rajabi F, Jabalameli N, Rezaei N. The Concept of Immunogenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:1-17. [DOI: 10.1007/978-3-030-92616-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Matejcic M, Patel Y, Lilyquist J, Hu C, Lee KY, Gnanaolivu RD, Hart SN, Polley EC, Yadav S, Boddicker NJ, Samara R, Xia L, Sheng X, Lubmawa A, Kiddu V, Masaba B, Namuguzi D, Mutema G, Job K, Henry DM, Ingles SA, Wilkens L, Le Marchand L, Watya S, Couch FJ, Conti DV, Haiman CA. Pathogenic Variants in Cancer Predisposition Genes and Prostate Cancer Risk in Men of African Ancestry. JCO Precis Oncol 2020; 4:32-43. [PMID: 32832836 DOI: 10.1200/po.19.00179] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PURPOSE In studies of men of European ancestry, rare pathogenic variants in DNA repair pathway genes have been shown to be associated with risk of aggressive prostate cancer. The contribution of rare coding variation to prostate cancer risk in men of African ancestry has not been established. METHODS We sequenced a panel of 19 DNA repair and cancer predisposition genes in 2,453 African American and 1,151 Ugandan prostate cancer cases and controls. Rare variants were classified as pathogenic or putatively functionally disruptive and examined in association with prostate cancer risk and disease aggressiveness in gene and pathway-level association analyses. RESULTS Pathogenic variants were found in 75 out of 2,098 cases (3.6%) and 31 out of 1,481 controls (2.1%) (OR=1.82, 95% CI=1.19 to 2.79, P=0.0044) with the association being stronger for more aggressive disease phenotypes (OR=3.10, 95% CI=1.54 to 6.23, P=0.0022). The highest risks for aggressive disease were observed with pathogenic variants in the ATM, BRCA2, PALB2 and NBN genes, with odds ratios ranging from ~4 to 15 in the combined study sample of African American and Ugandan men. Rare, non-pathogenic, non-synonymous variants did not have a major impact on risk of overall prostate cancer or disease aggressiveness. CONCLUSIONS Rare pathogenic variants in DNA repair genes have appreciable effects on risk of aggressive prostate cancer in men of African ancestry. These findings have potential implications for panel testing and risk stratification in this high-risk population.
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Affiliation(s)
- Marco Matejcic
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yesha Patel
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Kun Y Lee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Rohan D Gnanaolivu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Siddhartha Yadav
- Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicholas J Boddicker
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raed Samara
- QIAGEN Sciences, QIAGEN Inc., Frederick, Maryland 21703, USA
| | - Lucy Xia
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xin Sheng
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | | | | | - Dan Namuguzi
- Makerere University College of Health Sciences, Kampala 7072, Uganda
| | | | | | | | - Sue A Ingles
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Stephen Watya
- Uro Care, Kampala 25974, Uganda.,Makerere University College of Health Sciences, Kampala 7072, Uganda
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - David V Conti
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Genetic Study on Small Insertions and Deletions in Psoriasis Reveals a Role in Complex Human Diseases. J Invest Dermatol 2019; 139:2302-2312.e14. [PMID: 31078570 DOI: 10.1016/j.jid.2019.03.1157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 11/20/2022]
Abstract
Genetic studies based on single-nucleotide polymorphisms have provided valuable insights into the genetic architecture of complex diseases. However, a large fraction of heritability for most of these diseases remains unexplained, and the impact of small insertions and deletions (InDels) has been neglected. We performed a comprehensive screen on the exome sequence data of 1,326 genes using the SOAP-PopIndel method for InDels in 32,043 Chinese Han individuals and identified 29 unreported InDels within 25 susceptibility genes associated with psoriasis. Specifically, we identified 12 common, 9 low-frequency, and 8 rare InDels that explained approximately 1.29% of the heritability of psoriasis. Further analyses identified KIAA0319, RELN, NCAPG, ABO, AADACL2, LMAN1, FLG, HERC5, CCDC66, LEKR1, AFF3, ABCG2, ANXA7, SYTL2,GIPR, METTL1, and FYCO1 as unreported genes for psoriasis. In addition, identified InDels were associated with the following reported genes: IFIH1, ERAP1, ERAP2, LNPEP, UBLCP1, and STAT3; unreported independent associations for exonic InDels were found within GJB2 and ZNF816A. Our study enriched the genetic basis and pathogenesis of psoriasis and highlighted the non-negligible impact of InDels on complex human diseases.
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Shao H, Ganesamoorthy D, Duarte T, Cao MD, Hoggart CJ, Coin LJM. npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinformatics 2018; 19:261. [PMID: 30001702 PMCID: PMC6044046 DOI: 10.1186/s12859-018-2252-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 06/18/2018] [Indexed: 11/21/2022] Open
Abstract
Background Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. Result We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm the presence of two of these novel inversions. We show that there is a near linear relationship between the length of flanking IR and the minimum inversion size, without inverted repeats. Conclusion The application of npInv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion. Electronic supplementary material The online version of this article (10.1186/s12859-018-2252-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haojing Shao
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Devika Ganesamoorthy
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Tania Duarte
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Minh Duc Cao
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Clive J Hoggart
- Department of Medicine, Imperial College London, Level 2, Faculty Building South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Lachlan J M Coin
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia.
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Graphtyper enables population-scale genotyping using pangenome graphs. Nat Genet 2017; 49:1654-1660. [PMID: 28945251 DOI: 10.1038/ng.3964] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/01/2017] [Indexed: 12/30/2022]
Abstract
A fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.
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Rand KA, Rohland N, Tandon A, Stram A, Sheng X, Do R, Pasaniuc B, Allen A, Quinque D, Mallick S, Le Marchand L, Kaggwa S, Lubwama A, Stram DO, Watya S, Henderson BE, Conti DV, Reich D, Haiman CA. Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk. Hum Mol Genet 2015; 25:371-81. [PMID: 26604137 DOI: 10.1093/hmg/ddv462] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 11/06/2015] [Indexed: 12/31/2022] Open
Abstract
Prostate cancer is the most common non-skin cancer in males, with a ∼1.5-2-fold higher incidence in African American men when compared with whites. Epidemiologic evidence supports a large heritable contribution to prostate cancer, with over 100 susceptibility loci identified to date that can explain ∼33% of the familial risk. To explore the contribution of both rare and common variation in coding regions to prostate cancer risk, we sequenced the exomes of 2165 prostate cancer cases and 2034 controls of African ancestry at a mean coverage of 10.1×. We identified 395 220 coding variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest associations observed in SPARCL1 on 4q22.1 (rs13051, Ala49Asp, OR = 0.78, P = 1.8 × 10(-6)) and PTPRR on 12q15 (rs73341069, Val239Ile, OR = 1.62, P = 2.5 × 10(-5)). In gene-level testing, the two most significant genes were C1orf100 (P = 2.2 × 10(-4)) and GORAB (P = 2.3 × 10(-4)). We did not observe exome-wide significant associations (after correcting for multiple hypothesis testing) in single variant or gene-level testing in the overall case-control or case-case analyses of disease aggressiveness. In this first whole-exome sequencing study of prostate cancer, our findings do not provide strong support for the hypothesis that NS coding variants down to 0.5-1.0% frequency have large effects on prostate cancer risk in men of African ancestry. Higher-coverage sequencing efforts in larger samples will be needed to study rarer variants with smaller effect sizes associated with prostate cancer risk.
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Affiliation(s)
- Kristin A Rand
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex Stram
- Department of Preventive Medicine, Keck School of Medicine
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine
| | - Ron Do
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, Department of Human Genetics, David Geffen School of Medicine, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alex Allen
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dominique Quinque
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI 96813, USA
| | | | - Alex Lubwama
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda and
| | | | | | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen Watya
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda and Uro Care, Kampala, Uganda
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA,
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Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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Robert C, Fuentes-Utrilla P, Troup K, Loecherbach J, Turner F, Talbot R, Archibald AL, Mileham A, Deeb N, Hume DA, Watson M. Design and development of exome capture sequencing for the domestic pig (Sus scrofa). BMC Genomics 2014; 15:550. [PMID: 24988888 PMCID: PMC4099480 DOI: 10.1186/1471-2164-15-550] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig. Results We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels. Conclusions We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-550) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.
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Lucas-Lledó JI, Vicente-Salvador D, Aguado C, Cáceres M. Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm. BMC Bioinformatics 2014; 15:163. [PMID: 24884587 PMCID: PMC4055234 DOI: 10.1186/1471-2105-15-163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/14/2014] [Indexed: 11/21/2022] Open
Abstract
Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation, and they usually assume that the two alleles in a heterozygous individual are sampled with equal probability. This is generally false for structural variants detected with paired ends or split reads. Therefore, the population genetics of structural variants cannot be studied, unless a painstaking and potentially biased genotyping is performed first. Results We present svgem, an expectation-maximization implementation to estimate allele and genotype frequencies, calculate genotype posterior probabilities, and test for Hardy-Weinberg equilibrium and for population differences, from the numbers of times the alleles are observed in each individual. Although applicable to single nucleotide variation, it aims at bi-allelic structural variation of any type, observed by either split reads or paired ends, with arbitrarily high allele sampling bias. We test svgem with simulated and real data from the 1000 Genomes Project. Conclusions svgem makes it possible to use low-coverage sequencing data to study the population distribution of structural variants without having to know their genotypes. Furthermore, this advance allows the combined analysis of structural and nucleotide variation within the same genotype-free statistical framework, thus preventing biases introduced by genotype imputation.
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Affiliation(s)
- José Ignacio Lucas-Lledó
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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