Literature DB >> 22843986

zCall: a rare variant caller for array-based genotyping: genetics and population analysis.

Jacqueline I Goldstein1, Andrew Crenshaw, Jason Carey, George B Grant, Jared Maguire, Menachem Fromer, Colm O'Dushlaine, Jennifer L Moran, Kimberly Chambert, Christine Stevens, Pamela Sklar, Christina M Hultman, Shaun Purcell, Steven A McCarroll, Patrick F Sullivan, Mark J Daly, Benjamin M Neale.   

Abstract

SUMMARY: zCall is a variant caller specifically designed for calling rare single-nucleotide polymorphisms from array-based technology. This caller is implemented as a post-processing step after a default calling algorithm has been applied. The algorithm uses the intensity profile of the common allele homozygote cluster to define the location of the other two genotype clusters. We demonstrate improved detection of rare alleles when applying zCall to samples that have both Illumina Infinium HumanExome BeadChip and exome sequencing data available. AVAILABILITY: http://atguweb.mgh.harvard.edu/apps/zcall. CONTACT: bneale@broadinstitute.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mesh：

Year:  2012        PMID： 22843986      PMCID： PMC3463112          DOI： 10.1093/bioinformatics/bts479

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

Review 1.  Five years of GWAS discovery.

Authors:  Peter M Visscher; Matthew A Brown; Mark I McCarthy; Jian Yang
Journal:  Am J Hum Genet       Date:  2012-01-13       Impact factor: 11.025

2.  Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.

Authors:  S E Bergen; C T O'Dushlaine; S Ripke; P H Lee; D M Ruderfer; S Akterin; J L Moran; K D Chambert; R E Handsaker; L Backlund; U Ösby; S McCarroll; M Landen; E M Scolnick; P K E Magnusson; P Lichtenstein; C M Hultman; S M Purcell; P Sklar; P F Sullivan
Journal:  Mol Psychiatry       Date:  2012-06-12       Impact factor: 15.992

Review 3.  Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease.

Authors:  David Botstein; Neil Risch
Journal:  Nat Genet       Date:  2003-03       Impact factor: 38.330

4.  Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs.

Authors:  Joshua M Korn; Finny G Kuruvilla; Steven A McCarroll; Alec Wysoker; James Nemesh; Simon Cawley; Earl Hubbell; Jim Veitch; Patrick J Collins; Katayoon Darvishi; Charles Lee; Marcia M Nizzari; Stacey B Gabriel; Shaun Purcell; Mark J Daly; David Altshuler
Journal:  Nat Genet       Date:  2008-09-07       Impact factor: 38.330

5.  optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.

Authors:  T S Shah; J Z Liu; J A B Floyd; J A Morris; N Wirth; J C Barrett; C A Anderson
Journal:  Bioinformatics       Date:  2012-04-12       Impact factor: 6.937

6.  Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips.

Authors:  Matthew E Ritchie; Ruijie Liu; Benilton S Carvalho; Rafael A Irizarry
Journal:  BMC Bioinformatics       Date:  2011-03-08       Impact factor: 3.169
  6 in total
  114 in total

1.  Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray.

Authors:  Jonathan R I Coleman; Jack Euesden; Hamel Patel; Amos A Folarin; Stephen Newhouse; Gerome Breen
Journal:  Brief Funct Genomics       Date:  2015-10-05       Impact factor: 4.241

2.  Low-frequency coding variants at 6p21.33 and 20q11.21 are associated with lung cancer risk in Chinese populations.

Authors:  Guangfu Jin; Meng Zhu; Rong Yin; Wei Shen; Jia Liu; Jie Sun; Cheng Wang; Juncheng Dai; Hongxia Ma; Chen Wu; Zhihua Yin; Jiaqi Huang; Brandon W Higgs; Lin Xu; Yihong Yao; David C Christiani; Christopher I Amos; Zhibin Hu; Baosen Zhou; Yongyong Shi; Dongxin Lin; Hongbing Shen
Journal:  Am J Hum Genet       Date:  2015-04-30       Impact factor: 11.025

3.  Protective coding variants in CFH and PELI3 and a variant near CTRB1 are associated with age-related macular degeneration†.

Authors:  Yi Yu; Erin K Wagner; Eric H Souied; Sanna Seitsonen; Ilkka J Immonen; Paavo Häppölä; Soumya Raychaudhuri; Mark J Daly; Johanna M Seddon
Journal:  Hum Mol Genet       Date:  2016-12-01       Impact factor: 6.150

4.  Strategies for processing and quality control of Illumina genotyping arrays.

Authors:  Shilin Zhao; Wang Jing; David C Samuels; Quanghu Sheng; Yu Shyr; Yan Guo
Journal:  Brief Bioinform       Date:  2018-09-28       Impact factor: 11.622

5.  SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function.

Authors:  Man Li; Yong Li; Olivia Weeks; Vladan Mijatovic; Alexander Teumer; Jennifer E Huffman; Gerard Tromp; Christian Fuchsberger; Mathias Gorski; Leo-Pekka Lyytikäinen; Teresa Nutile; Sanaz Sedaghat; Rossella Sorice; Adrienne Tin; Qiong Yang; Tarunveer S Ahluwalia; Dan E Arking; Nathan A Bihlmeyer; Carsten A Böger; Robert J Carroll; Daniel I Chasman; Marilyn C Cornelis; Abbas Dehghan; Jessica D Faul; Mary F Feitosa; Giovanni Gambaro; Paolo Gasparini; Franco Giulianini; Iris Heid; Jinyan Huang; Medea Imboden; Anne U Jackson; Janina Jeff; Min A Jhun; Ronit Katz; Annette Kifley; Tuomas O Kilpeläinen; Ashish Kumar; Markku Laakso; Ruifang Li-Gao; Kurt Lohman; Yingchang Lu; Reedik Mägi; Giovanni Malerba; Evelin Mihailov; Karen L Mohlke; Dennis O Mook-Kanamori; Antonietta Robino; Douglas Ruderfer; Erika Salvi; Ursula M Schick; Christina-Alexandra Schulz; Albert V Smith; Jennifer A Smith; Michela Traglia; Laura M Yerges-Armstrong; Wei Zhao; Mark O Goodarzi; Aldi T Kraja; Chunyu Liu; Jennifer Wessel; Eric Boerwinkle; Ingrid B Borecki; Jette Bork-Jensen; Erwin P Bottinger; Daniele Braga; Ivan Brandslund; Jennifer A Brody; Archie Campbell; David J Carey; Cramer Christensen; Josef Coresh; Errol Crook; Gary C Curhan; Daniele Cusi; Ian H de Boer; Aiko P J de Vries; Joshua C Denny; Olivier Devuyst; Albert W Dreisbach; Karlhans Endlich; Tõnu Esko; Oscar H Franco; Tibor Fulop; Glenn S Gerhard; Charlotte Glümer; Omri Gottesman; Niels Grarup; Vilmundur Gudnason; Torben Hansen; Tamara B Harris; Caroline Hayward; Lynne Hocking; Albert Hofman; Frank B Hu; Lise Lotte N Husemoen; Rebecca D Jackson; Torben Jørgensen; Marit E Jørgensen; Mika Kähönen; Sharon L R Kardia; Wolfgang König; Charles Kooperberg; Jennifer Kriebel; Lenore J Launer; Torsten Lauritzen; Terho Lehtimäki; Daniel Levy; Pamela Linksted; Allan Linneberg; Yongmei Liu; Ruth J F Loos; Antonio Lupo; Christine Meisinger; Olle Melander; Andres Metspalu; Paul Mitchell; Matthias Nauck; Peter Nürnberg; Marju Orho-Melander; Afshin Parsa; Oluf Pedersen; Annette Peters; Ulrike Peters; Ozren Polasek; David Porteous; Nicole M Probst-Hensch; Bruce M Psaty; Lu Qi; Olli T Raitakari; Alex P Reiner; Rainer Rettig; Paul M Ridker; Fernando Rivadeneira; Jacques E Rossouw; Frank Schmidt; David Siscovick; Nicole Soranzo; Konstantin Strauch; Daniela Toniolo; Stephen T Turner; André G Uitterlinden; Sheila Ulivi; Dinesh Velayutham; Uwe Völker; Henry Völzke; Melanie Waldenberger; Jie Jin Wang; David R Weir; Daniel Witte; Helena Kuivaniemi; Caroline S Fox; Nora Franceschini; Wolfram Goessling; Anna Köttgen; Audrey Y Chu
Journal:  J Am Soc Nephrol       Date:  2016-12-05       Impact factor: 10.121

6.  Identification of type 2 diabetes subgroups through topological analysis of patient similarity.

Authors:  Li Li; Wei-Yi Cheng; Benjamin S Glicksberg; Omri Gottesman; Ronald Tamler; Rong Chen; Erwin P Bottinger; Joel T Dudley
Journal:  Sci Transl Med       Date:  2015-10-28       Impact factor: 17.956

7.  Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs.

Authors:  Giorgio Pistis; Eleonora Porcu; Scott I Vrieze; Carlo Sidore; Maristella Steri; Fabrice Danjou; Fabio Busonero; Antonella Mulas; Magdalena Zoledziewska; Andrea Maschio; Christine Brennan; Sandra Lai; Michael B Miller; Marco Marcelli; Maria Francesca Urru; Maristella Pitzalis; Robert H Lyons; Hyun M Kang; Chris M Jones; Andrea Angius; William G Iacono; David Schlessinger; Matt McGue; Francesco Cucca; Gonçalo R Abecasis; Serena Sanna
Journal:  Eur J Hum Genet       Date:  2014-10-08       Impact factor: 4.246

8.  No large-effect low-frequency coding variation found for myocardial infarction.

Authors:  Oddgeir L Holmen; He Zhang; Wei Zhou; Ellen Schmidt; Daniel H Hovelson; Arnulf Langhammer; Maja-Lisa Løchen; Santhi K Ganesh; Ellisiv B Mathiesen; Lars Vatten; Carl Platou; Tom Wilsgaard; Jin Chen; Frank Skorpen; Håvard Dalen; Michael Boehnke; Goncalo R Abecasis; Inger Njølstad; Kristian Hveem; Cristen J Willer
Journal:  Hum Mol Genet       Date:  2014-04-12       Impact factor: 6.150

9.  Genome-Wide Association Studies of Metabolites in Patients with CKD Identify Multiple Loci and Illuminate Tubular Transport Mechanisms.

Authors:  Yong Li; Peggy Sekula; Matthias Wuttke; Judith Wahrheit; Birgit Hausknecht; Ulla T Schultheiss; Wolfram Gronwald; Pascal Schlosser; Sara Tucci; Arif B Ekici; Ute Spiekerkoetter; Florian Kronenberg; Kai-Uwe Eckardt; Peter J Oefner; Anna Köttgen
Journal:  J Am Soc Nephrol       Date:  2018-03-15       Impact factor: 10.121

10.  The genetic associations of acute anterior uveitis and their overlap with the genetics of ankylosing spondylitis.

Authors:  P C Robinson; P J Leo; J J Pointon; J Harris; K Cremin; L A Bradbury; S Stebbings; A A Harrison; D M Evans; E L Duncan; B P Wordsworth; M A Brown
Journal:  Genes Immun       Date:  2015-11-26       Impact factor: 2.676
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