A beginners guide to SNP calling from high-throughput DNA-sequencing data.

Abstract:

:High-throughput DNA sequencing (HTS) is of increasing importance in the life sciences. One of its most prominent applications is the sequencing of whole genomes or targeted regions of the genome such as all exonic regions (i.e., the exome). Here, the objective is the identification of genetic variants such as single nucleotide polymorphisms (SNPs). The extraction of SNPs from the raw genetic sequences involves many processing steps and the application of a diverse set of tools. We review the essential building blocks for a pipeline that calls SNPs from raw HTS data. The pipeline includes quality control, mapping of short reads to the reference genome, visualization and post-processing of the alignment including base quality recalibration. The final steps of the pipeline include the SNP calling procedure along with filtering of SNP candidates. The steps of this pipeline are accompanied by an analysis of a publicly available whole-exome sequencing dataset. To this end, we employ several alignment programs and SNP calling routines for highlighting the fact that the choice of the tools significantly affects the final results.

journal_name

Hum Genet

journal_title

Human genetics

authors

Altmann A,Weber P,Bader D,Preuss M,Binder EB,Müller-Myhsok B

doi

10.1007/s00439-012-1213-z

subject

Has Abstract

pub_date

2012-10-01 00:00:00

pages

1541-54

issue

10

eissn

0340-6717

issn

1432-1203

journal_volume

131

pub_type

杂志文章,评审
  • BglII RFLP in DXS 498 between the pigment gene repeat unit, RCP and GCP.

    abstract::The red (RCP) and green (GCP) color pigment genes are located in Xq28, a chromosomal region implicated in many genetic disorders. The restriction fragment length polymorphism (RFLP) we describe here will be useful for linkage analysis in these disorders. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00220092

    authors: Vits L,Willems PJ

    更新日期:1992-11-01 00:00:00

  • "Complete" trisomy 5p; de novo translocation t(2;5)(q36;p11) with isochromosome 5p. Case report and review of the literature.

    abstract::A case of complete trisomy 5p due to a de novo translocation t(2;5)(q36;p11) with an isochromosome 5p is described. Complete trisomy 5p has been reported only once (Brimblecombe et al., 1977). The confusing literature relating to partial trisomy 5p is reviewed. Comparison of our case with the patients reported by Brim...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00273310

    authors: Leschot NJ,Lim KS

    更新日期:1979-02-15 00:00:00

  • Genetic variation of hexosaminidase A and arylsulfatase A activity. Correlation study in amnio-maternal pairs of cultured cells.

    abstract::Pairs of cultured amniotic cells and maternal fibroblasts ("feto-maternal pairs") were studied for hexosaminidase A (HXA) and arylsulfatase A (ASA) activity. These lysosomal enzyme activities are genetically deficient in Tay-Sachs disease and metachromatic leukodystrophy, respectively. After HXA was standardized by re...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00281692

    authors: Harzer K,Hayashi K

    更新日期:1981-01-01 00:00:00

  • Translocation t(1;17)(q12;q25) with a clinical picture like of a proximal deletion of 1q: identification by in situ hybridization with chromosome 1-specific satellite DNA probes.

    abstract::The authors report a case of a balanced 1;17 translocation with breakpoints located in the secondary constriction of chromosome 1. This translocation is associated with pathological symptoms similar to those observed following a proximal deletion of 1q. We request contact with colleques who have observed similar, or r...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00197700

    authors: Vorsanova SG,Yurov YB,Kurbatov MB,Kazantzeva LZ

    更新日期:1990-12-01 00:00:00

  • Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia.

    abstract::Trust may be important in shaping public attitudes to genetics and intentions to participate in genomics research and big data initiatives. As such, we examined trust in data sharing among the general public. A cross-sectional online survey collected responses from representative publics in the USA, Canada, UK and Aus...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-019-02062-0

    authors: Milne R,Morley KI,Howard H,Niemiec E,Nicol D,Critchley C,Prainsack B,Vears D,Smith J,Steed C,Bevan P,Atutornu J,Farley L,Goodhand P,Thorogood A,Kleiderman E,Middleton A,Participant Values Work Stream of the Global Allia

    更新日期:2019-12-01 00:00:00

  • B-cell-negative severe combined immunodeficiency associated with a common gamma chain mutation.

    abstract::Severe combined immunodeficiency (SCID) is caused by a variety of underlying defects. Approximately 40% of cases are thought to be of the X-linked type (SCIDX1), which is phenotypically characterised by the absence, or very low numbers, of T cells, but normal or even high B cell numbers. The gene responsible for SCIDX...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050428

    authors: Jones AM,Clark PA,Katz F,Genet S,McMahon C,Alterman L,Cant A,Kinnon C

    更新日期:1997-05-01 00:00:00

  • A review of gene-by-air pollution interactions for cardiovascular disease, risk factors, and biomarkers.

    abstract::Air pollution is recognized as causal factor for cardiovascular disease (CVD) and is associated with multiple CVD risk factors. Substantial research effort has been invested in understanding the linkages between genetic variation and CVD risk, resulting in over 50 CVD-associated genetic loci. More recently, gene-air p...

    journal_title:Human genetics

    pub_type: 杂志文章,评审

    doi:10.1007/s00439-019-02004-w

    authors: Ward-Caviness CK

    更新日期:2019-06-01 00:00:00

  • Linkage between the loci for the Lp(a) lipoprotein (LP) and plasminogen (PLG).

    abstract::A locus, LP, that determines quantitative variation of Lp(a) lipoprotein phenotypes is linked to the plasminogen (PLG) locus (peak lod score = 12.73). This linkage relationship assigns a locus with alleles that have an affect on risk for coronary artery disease to the long arm of chromosome 6. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00291716

    authors: Weitkamp LR,Guttormsen SA,Schultz JS

    更新日期:1988-05-01 00:00:00

  • Monosomy 21 in a human spontaneous abortus. Morphogenetic disturbances and phenotype at the cellular level.

    abstract::Complex investigation of a spontaneous abortus with monosomy 21 was carried out. Phenotypic expression at the organism and tissue level was characterized by the pathology of the external form of the embryo and by abnormalities of the embryonic facial structures, the stomodeum, the anterior part of the primary gut, and...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00527395

    authors: Kuliev AM,Grinberg KN,Kukharenko VI,Kulazenko VP,Bogomazov EA

    更新日期:1977-09-22 00:00:00

  • Complement component C3: molecular basis of the C3*S025 variant and evidence for molecular heterogeneity of other variants.

    abstract::Complement component 3 (C3) is the central molecule of the complement system. It displays a number of polymorphic variants with, as yet, unclear functional consequences. We have investigated a number of rare C3 variants by PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism) analysis and could ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00197408

    authors: Höhler T,Botto M,Rittner C,Schneider PM,Meyer zum Büschenfelde KH

    更新日期:1995-11-01 00:00:00

  • Fetal gender determination in early pregnancy through qualitative and quantitative analysis of fetal DNA in maternal serum.

    abstract::Fetal DNA in maternal plasma and serum has been shown to be a useful material for fetal gender determination and for screening tests for abnormal pregnancies except during early gestational ages. Maternal serum samples were obtained from 81 pregnant women during the 5th-10th weeks of gestation. Fetal gender was determ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-001-0649-3

    authors: Honda H,Miharu N,Ohashi Y,Samura O,Kinutani M,Hara T,Ohama K

    更新日期:2002-01-01 00:00:00

  • X-linked agammaglobulinemia and the red blood cell determinants Xg and 12E7 are not closely linked.

    abstract::Studies on the segregation of the red blood cell determinant Xg in 12 families with X-linked inheritance of agammaglobulinemia (XLA) in 3-4 generations suggested linkage of Xg with XLA. One extensive pedigree of a Dutch family with XLA in eight generations was investigated for Xg and the quantitative polymorphism 12E7...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00292589

    authors: Mensink EJ,Schot JD,Tippett P,Ott J,Schuurman RK

    更新日期:1984-01-01 00:00:00

  • Localization of the human oncogene SPI1 on chromosome 11, region p11.22.

    abstract::Spi1 is an oncogene specifically activated in acute murine erythroleukemias induced by the Friend spleen focus forming virus (SFFV). Three probes were used for the chromosomal assignment of the human SPI1 oncogene: cDb1 and RaB2 correspond respectively to murine Spi1 and human SPI1 cDNA probes; C45a6B probe is a murin...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00210807

    authors: Nguyen VC,Ray D,Gross MS,de Tand MF,Frézal J,Moreau-Gachelin F

    更新日期:1990-05-01 00:00:00

  • Variation in estimated recombination rates across human populations.

    abstract::Recently it has been reported that recombination hotspots appear to be highly variable between humans and chimpanzees, and there is evidence for between-person variability in hotspots, and evolutionary transience. To understand the nature of variation in human recombination rates, it is important to describe patterns ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-007-0391-6

    authors: Graffelman J,Balding DJ,Gonzalez-Neira A,Bertranpetit J

    更新日期:2007-11-01 00:00:00

  • Genetic background of apparently idiopathic sporadic cerebellar ataxia.

    abstract::Disease-causing mutations have been identified in various entities of autosomal dominant ataxia and in Friedreich's ataxia. However, no molecular pathogenic factor is known to cause idiopathic cerebellar ataxias. We investigated the CAG/CTG trinucleotide repeats causing spinocerebellar ataxia types 1, 2, 3, 6, 7, 8 an...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390000346

    authors: Schöls L,Szymanski S,Peters S,Przuntek H,Epplen JT,Hardt C,Riess O

    更新日期:2000-08-01 00:00:00

  • Genetic complementation of steroid sulphatase after somatic cell hybridization of X-linked ichthyosis and multiple sulphatase deficiency.

    abstract::Complementation studies of steroid sulphatase were carried out in the heterokaryon population of fibroblasts derived from patients with X-linked ichthyosis and multiple sulphatase deficiency. The activity of steroid sulphatase of the fused cell population was constantly higher (approximately 2-5 fold) than that of the...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00295367

    authors: Ballabio A,Parenti G,Napolitano E,Di Natale P,Andria G

    更新日期:1985-01-01 00:00:00

  • Logistic regression model to estimate the risk of unbalanced offspring in reciprocal translocations.

    abstract::The aim of this study was to estimate the risk of viable unbalanced offspring for a parental carrier of reciprocal translocation. On a large computerized database of reciprocal translocations we used logistic regression to model this risk. The status of the progeny is the outcome variable. Explanatory covariates are c...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00420946

    authors: Cans C,Cohen O,Lavergne C,Mermet MA,Demongeot J,Jalbert P

    更新日期:1993-12-01 00:00:00

  • Highly polymorphic dinucleotide repeat at the NF2 gene.

    abstract::A highly polymorphic CA repeat was identified in a cosmid containing the 5' end of the NF2 tumour suppressor gene. This marker has proved useful in presymptomatic diagnosis in affected families. ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00209494

    authors: Bourn D,Strachan T

    更新日期:1995-06-01 00:00:00

  • SMN gene duplication and the emergence of the SMN2 gene occurred in distinct hominids: SMN2 is unique to Homo sapiens.

    abstract::The spinal muscular atrophy (SMA) region on chromosome 5q13 contains an inverted duplication of about 500 kb, and deleterious mutations in the survival motor neuron 1 (SMN1) gene cause SMA, a common lethal childhood neuropathy. We have used a number of approaches to probe the evolutionary history of these genes and sh...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390100473

    authors: Rochette CF,Gilbert N,Simard LR

    更新日期:2001-03-01 00:00:00

  • Carrier and prenatal diagnosis of X-linked severe combined immunodeficiency: mutation detection methods and utilization.

    abstract::IL2RG, the gene encoding the common gamma chain, gamma c, of the receptor for interleukin-2 and other cytokines, has been identified as the disease gene for severe combined immunodeficiency (SCID) of the X-linked type. Specific mutational diagnosis for X-linked SCID has thus become possible. For many women at risk for...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050418

    authors: Puck JM,Middelton L,Pepper AE

    更新日期:1997-05-01 00:00:00

  • Polyploidies in abortion material decrease with maternal age.

    abstract::Among 639 spontaneous abortions between the 8th and 14th week of gestation 342 (53.5%) revealed an abnormal karyotype. While the rate of trisomies distinctly increased with advancing maternal age, a decrease in the rate of 45,X conceptuses and polyploidies was observed among abortions from older women. The overall rel...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00205080

    authors: Neuber M,Rehder H,Zuther C,Lettau R,Schwinger E

    更新日期:1993-07-01 00:00:00

  • Genetic characterization of congenital tufting enteropathy: epcam associated phenotype and involvement of SPINT2 in the syndromic form.

    abstract::Congenital tufting enteropathy (CTE) is a rare and severe enteropathy recently ascribed to mutations in the epcam gene. Here we establish SPINT2, previously ascribed to congenital sodium diarrhea, as a second gene associated with CTE and report molecular and immunohistochemistry data in 57 CTE patients. Inclusion crit...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-013-1380-6

    authors: Salomon J,Goulet O,Canioni D,Brousse N,Lemale J,Tounian P,Coulomb A,Marinier E,Hugot JP,Ruemmele F,Dufier JL,Roche O,Bodemer C,Colomb V,Talbotec C,Lacaille F,Campeotto F,Cerf-Bensussan N,Janecke AR,Mueller T,Kolet

    更新日期:2014-03-01 00:00:00

  • A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence.

    abstract::Gene-gene and gene-environment interactions govern a substantial portion of the variation in complex traits and diseases. In convention, a set of either unrelated or family samples are used in detection of such interactions; even when both kinds of data are available, the unrelated and the family samples are analyzed ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-013-1361-9

    authors: Chen GB,Liu N,Klimentidis YC,Zhu X,Zhi D,Wang X,Lou XY

    更新日期:2014-02-01 00:00:00

  • Genetic and epigenetic Muller's ratchet as a mechanism of frailty and morbidity during aging: a demographic genetic model.

    abstract::Mutation accumulation has been proposed as a cause of senescence. During this process, age-related genetic and epigenetic mutations steadily accumulate. Cascading deleterious effects of mutations might initiate a steady "accumulation of deficits" in cells, despite the existence of repair mechanisms, leading to cellula...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-019-02067-9

    authors: Innan H,Veitia R,Govindaraju DR

    更新日期:2020-03-01 00:00:00

  • Nine novel germline mutations of STK11 in ten families with Peutz-Jeghers syndrome.

    abstract::Peutz-Jeghers Syndrome (PJS) is an autosomal dominant hereditary disease characterized by hamartomatous polyposis involving the entire bowel. Recently STK11, a gene bearing a mutation responsible for PJS, was isolated. We investigated the entire coding region of STK11 in 15 unrelated PJS families by the PCR-SSCP (poly...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s004390050801

    authors: Nakagawa H,Koyama K,Miyoshi Y,Ando H,Baba S,Watatani M,Yasutomi M,Matsuura N,Monden M,Nakamura Y

    更新日期:1998-08-01 00:00:00

  • Co-segregation of trichorhinophalangeal syndrome with a t(8;13)(q23.3;q21.31) familial translocation that appears to increase TRPS1 gene expression.

    abstract::Trichorhinophalangeal syndrome type I (TRPS I) is a rare autosomal dominant syndrome caused by haploinsufficiency of TRPS1 due to point mutations or deletions. Here, we report the first familial TRPS I due to a t(8;13)(q23.3;q21.31) translocation breakpoint <100 kb from the 5' end of TRPS1. Based on the additional abn...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-013-1333-0

    authors: David D,Marques B,Ferreira C,Araújo C,Vieira L,Soares G,Dias C,Pinto M

    更新日期:2013-11-01 00:00:00

  • Localization of the human GLO gene locus.

    abstract::Data on the linkage relation between the GLO locus and the HLA, Bf, and PGM3 loci are presented. The family material includes 49 GLO/HLA-B (and/or Bf) segregating matings with 134 children informative on 199 parental meioses. Of phase-known meioses, 3 are recombinants and 75 nonrecombinants; linkage is therefore prove...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00295820

    authors: Olaisen B,Gedde-Dahl T Jr,Thorsby E

    更新日期:1976-06-29 00:00:00

  • Mechanisms for phenotypic variation in Lesch-Nyhan disease and its variants.

    abstract::Lesch-Nyhan disease is a neurogenetic disorder caused by mutation of the HPRT1 gene on the X chromosome. There is significant variation in the clinical phenotype, with more than 300 different known mutations. There are few studies that have addressed whether similar mutations result in similar phenotypes across differ...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-010-0901-9

    authors: Sampat R,Fu R,Larovere LE,Torres RJ,Ceballos-Picot I,Fischbach M,de Kremer R,Schretlen DJ,Puig JG,Jinnah HA

    更新日期:2011-01-01 00:00:00

  • Characterization of mitochondrial haplogroups in a large population-based sample from the United States.

    abstract::Mitochondrial DNA (mtDNA) haplogroups are valuable for investigations in forensic science, molecular anthropology, and human genetics. In this study, we developed a custom panel of 61 mtDNA markers for high-throughput classification of European, African, and Native American/Asian mitochondrial haplogroup lineages. Usi...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/s00439-014-1421-9

    authors: Mitchell SL,Goodloe R,Brown-Gentry K,Pendergrass SA,Murdock DG,Crawford DC

    更新日期:2014-07-01 00:00:00

  • Polymerase chain reaction amplification of two polymorphic simple repeat sequences within the von Willebrand factor gene: application to family studies in von Willebrand disease.

    abstract::We have used the polymerase chain reaction to amplify two variable number of tandem repeats (VNTRs) within a region of repetitive DNA located in intron 40 of the von Willebrand factor (vWf) gene. Heterozygosity for VNTR I was observed in 30 out of 39 normal unrelated individuals tested (77%), and for VNTR II in 29 out...

    journal_title:Human genetics

    pub_type: 杂志文章

    doi:10.1007/BF00217122

    authors: Cumming AM,Armstrong JG,Pendry K,Burn AM,Wensley RT

    更新日期:1992-05-01 00:00:00