Next-generation sequencing approaches for genetic mapping of complex diseases

The advent of next generation sequencing technologies has opened new possibilities in the analysis of human disease. In this review we present the main next-generation sequencing technologies, with their major contributions and possible applications to the study of the genetic etiology of complex diseases.

[1]  Suzanne M. Leal,et al.  Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies , 2009, PLoS genetics.

[2]  R. Plenge.  GWASs and the age of human as the model organism for autoimmune genetic research , 2010, Genome Biology.

[3]  Alexander R. Griffing,et al.  Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. , 2010, American journal of human genetics.

[4]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[5]  Stephen L. Hauser,et al.  Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis , 2010, Nature.

[6]  Ludwig Kappos,et al.  Genome-wide association study in a high-risk isolate for multiple sclerosis reveals associated variants in STAT3 gene. , 2010, American journal of human genetics.

[7]  D. Goldstein,et al.  Uncovering the roles of rare variants in common disease through whole-genome sequencing , 2010, Nature Reviews Genetics.

[8]  Shamil R Sunyaev,et al.  Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. , 2007, American journal of human genetics.

[9]  Momiao Xiong,et al.  Association studies for next-generation sequencing. , 2011, Genome research.

[10]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[11]  P. Shannon,et al.  Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.

[12]  John C. Marioni,et al.  Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data , 2009, Bioinform..

[13]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[14]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[15]  D. Clayton,et al.  Improved power offered by a score test for linkage disequilibrium mapping of quantitative-trait loci by selective genotyping. , 2006, American journal of human genetics.

[16]  Paul J. Rathouz,et al.  An Evolutionary Framework for Association Testing in Resequencing Studies , 2010, PLoS genetics.

[17]  Zhenyu Xuan,et al.  Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing , 2009, Nature Protocols.

[18]  F. Rieux-Laucat,et al.  Whole-exome-sequencing-based discovery of human FADD deficiency. , 2010, American journal of human genetics.

[19]  S. Quake,et al.  Sequence information can be obtained from single DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  A. Misra,et al.  SNP genotyping: technologies and biomedical applications. , 2007, Annual review of biomedical engineering.

[21]  M. Nachman,et al.  Estimate of the mutation rate per nucleotide in humans. , 2000, Genetics.

[22]  Sebastian Bauer,et al.  Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome , 2010, Nature Genetics.

[23]  Detlef Weigel,et al.  Deep sequencing to reveal new variants in pooled DNA samples , 2009, Human mutation.

[24]  Sharon R Grossman,et al.  Integrating common and rare genetic variation in diverse human populations , 2010, Nature.

[25]  Rafael A Irizarry,et al.  Overcoming bias and systematic errors in next generation sequencing data , 2010, Genome Medicine.

[26]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[27]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[28]  David T. Okou,et al.  Microarray-based genomic selection for high-throughput resequencing , 2007, Nature Methods.

[29]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[30]  S. Browning,et al.  A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic , 2009, PLoS genetics.

[31]  Pablo Moscato,et al.  Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20 , 2009, Nature Genetics.

[32]  S. Leal,et al.  Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. , 2008, American journal of human genetics.

[33]  Xin Jin,et al.  TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. , 2010, Brain : a journal of neurology.

[34]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[35]  Robert B. Hartlage,et al.  This PDF file includes: Materials and Methods , 2009 .

[36]  Nada Jabado,et al.  Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next‐generation exome sequencing , 2010, Human mutation.

[37]  J. Sebat,et al.  Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders. , 2009, Trends in genetics : TIG.

[38]  Christian Gilissen,et al.  A de novo paradigm for mental retardation , 2010, Nature Genetics.

[39]  Carlos D. Bustamante,et al.  The cost of inbreeding in Arabidopsis , 2002, Nature.

[40]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[41]  Cole Trapnell,et al.  How to map billions of short reads onto genomes , 2009, Nature Biotechnology.

[42]  J. Todd,et al.  Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes , 2009, Science.

[43]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[44]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[45]  Paul Medvedev,et al.  Computational methods for discovering structural variation with next-generation sequencing , 2009, Nature Methods.

[46]  S. Turner,et al.  Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.

[47]  A. Singleton,et al.  Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia , 2008, Science.

[48]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[49]  Christian Gilissen,et al.  Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. , 2010, American journal of human genetics.

[50]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[51]  J. Lupski,et al.  The complete genome of an individual by massively parallel DNA sequencing , 2008, Nature.

[52]  Simon C. Potter,et al.  Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis , 2011, Nature.

[53]  Huanming Yang,et al.  Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree , 2009, Current Biology.

[54]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[55]  Tom Walsh,et al.  Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. , 2010, American journal of human genetics.

[56]  Simon C. Potter,et al.  Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants , 2007, Nature Genetics.

[57]  Gianmauro Cuccuru,et al.  Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis , 2010, Nature Genetics.

[58]  M. Spitz,et al.  Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. , 2008, American journal of human genetics.

[59]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[60]  Vikas Bansal,et al.  Efficient and Cost Effective Population Resequencing by Pooling and In-Solution Hybridization , 2011, PloS one.

[61]  J. Marchini,et al.  Genotype imputation for genome-wide association studies , 2010, Nature Reviews Genetics.

[62]  Margaret A. Pericak-Vance,et al.  Exome Sequencing of a Multigenerational Human Pedigree , 2009, PloS one.

[63]  E. D. Hyman.  A new method of sequencing DNA. , 1988, Analytical biochemistry.

[64]  H. Hakonarson,et al.  Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. , 2011, American journal of human genetics.

[65]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[66]  T. Walsh,et al.  MASP1 mutations in patients with facial, umbilical, coccygeal, and auditory findings of Carnevale, Malpuech, OSA, and Michels syndromes. , 2010, American journal of human genetics.

[67]  Jamie K Teer,et al.  Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. , 2010, American journal of human genetics.

[68]  Chiara Sabatti,et al.  Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses. , 2006, Human molecular genetics.

[69]  M. G. Reese,et al.  A probabilistic disease-gene finder for personal genomes. , 2011, Genome research.

[70]  Yudi Pawitan,et al.  Revisiting Mendelian disorders through exome sequencing , 2011, Human Genetics.

[71]  Fabio Macciardi,et al.  Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. , 2010, American journal of human genetics.

[72]  Emily H Turner,et al.  Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes , 2009, Nature.

[73]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[74]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[75]  G. Weinstock,et al.  Direct selection of human genomic loci by microarray hybridization , 2007, Nature Methods.

[76]  M. Slatkin.  Disequilibrium mapping of a quantitative-trait locus in an expanding population. , 1999, American journal of human genetics.

[77]  Toshihiro Tanaka.  The International HapMap Project , 2003, Nature.

[78]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[79]  Joshua M. Korn,et al.  Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease , 2011, Nature Genetics.

[80]  M. Beier,et al.  Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays , 2009, Analytical and bioanalytical chemistry.

[81]  D. Rujescu,et al.  Evidence for rare and common genetic risk variants for schizophrenia at protein kinase C, alpha , 2010, Molecular Psychiatry.

[82]  M. Metzker.  Sequencing in real time , 2009, Nature Biotechnology.

[83]  Sebastian Bauer,et al.  Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders , 2011, Bioinform..

[84]  Edouard Henrion,et al.  A Population Genetic Approach to Mapping Neurological Disorder Genes Using Deep Resequencing , 2011, PLoS genetics.

[85]  Lee-Jen Wei,et al.  Pooled Association Tests for Rare Variants in Exon-Resequencing Studies , 2010 .

[86]  Tao Wang,et al.  Resequencing of pooled DNA for detecting disease associations with rare variants , 2010, Genetic epidemiology.

[87]  Emily H Turner,et al.  Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome , 2010, Nature Genetics.

[88]  Joshua S. Paul,et al.  Genotype and SNP calling from next-generation sequencing data , 2011, Nature Reviews Genetics.

[89]  M. Rieder,et al.  Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations , 2011, Nature Genetics.

[90]  I. Tikhonova,et al.  Genetic diagnosis by whole exome capture and massively parallel DNA sequencing , 2009, Proceedings of the National Academy of Sciences.

[91]  Philip M. Kim,et al.  Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome , 2007, Science.

[92]  Mohsin Shahzad,et al.  Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. , 2010, American journal of human genetics.

[93]  Justin C. Fay,et al.  Quantification of rare allelic variants from pooled genomic DNA , 2009, Nature Methods.

[94]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[95]  M. Rivas,et al.  Nature Genetics Advance Online Publication High-throughput, Pooled Sequencing Identifies Mutations in Nubpl and Foxred1 in Human Complex I Deficiency , 2022 .

[96]  Alexey S Kondrashov,et al.  Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases , 2003, Human mutation.

[97]  M. Stephens,et al.  Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits , 2007, PLoS genetics.

[98]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[99]  Gang Shi,et al.  Optimum designs for next‐generation sequencing to discover rare variants for common complex disease , 2011, Genetic epidemiology.

[100]  S. Lok,et al.  Increased exonic de novo mutation rate in individuals with schizophrenia , 2011, Nature Genetics.

[101]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[102]  Michael R. Johnson,et al.  Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. , 2009, Human molecular genetics.

[103]  A. Hoischen,et al.  Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy. , 2010, American journal of human genetics.

[104]  J. Seidman,et al.  Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection , 2009, Nature Methods.

[105]  Kevin C. H. Ha,et al.  Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. , 2010, American journal of human genetics.

[106]  Kathryn Roeder,et al.  Testing for an Unusual Distribution of Rare Variants , 2011, PLoS genetics.

[107]  Gang Zheng,et al.  Linkage disequilibrium mapping of quantitative-trait Loci by selective genotyping. , 2005, American journal of human genetics.

[108]  L. Vécsei,et al.  The epidemiology of multiple sclerosis in Europe , 2006, European journal of neurology.

[109]  M. DePristo,et al.  Variation in genome-wide mutation rates within and between human families , 2011, Nature Genetics.

[110]  Paul Flicek,et al.  The functional spectrum of low-frequency coding variation , 2011, Genome Biology.

[111]  D. Conti,et al.  Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies , 2011, Genetic epidemiology.

[112]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[113]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

[114]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[115]  A. Sidow,et al.  Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. , 2005, Genome research.

[116]  Reed A. Cartwright,et al.  A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data , 2012, Statistical applications in genetics and molecular biology.

[117]  Jonathan M. Mudge,et al.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.

[118]  Gary D Bader,et al.  Functional impact of global rare copy number variation in autism spectrum disorders , 2010, Nature.

[119]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[120]  S. Quake,et al.  Single-Molecule DNA Sequencing of a Viral Genome , 2008, Science.

[121]  J. Gall,et al.  Human Genome Sequencing , 1986, Science.

[122]  D. Craig,et al.  Identification of a Novel Risk Locus for Multiple Sclerosis at 13q31.3 by a Pooled Genome-Wide Scan of 500,000 Single Nucleotide Polymorphisms , 2008, PloS one.

[123]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[124]  Jonathan C. Cohen,et al.  Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. , 2010, The New England journal of medicine.

[125]  M. Lynch.  Rate, molecular spectrum, and consequences of human mutation , 2010, Proceedings of the National Academy of Sciences.

[126]  P. Shannon,et al.  Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing , 2010, Science.

[127]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[128]  A. Hoischen,et al.  STAT1 mutations in autosomal dominant chronic mucocutaneous candidiasis. , 2011, The New England journal of medicine.

[129]  C I Amos,et al.  Evolutionary evidence of the effect of rare variants on disease etiology , 2011, Clinical genetics.