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Literature DB >> 18854868

SNP frequency estimation using massively parallel sequencing of pooled DNA.

Abstract

Resequencing of genomic regions that have been implicated by linkage and/or association studies to harbor genetic susceptibility loci represents a necessary step to identify causal variants. Massively parallel sequencing (MPS) offers the possibility of SNP discovery and frequency determination among pooled DNA samples. The strategies of pooling DNA samples and pooling PCR amplicons generated from individual DNA samples were evaluated, and both were found to return accurate estimates of SNP frequencies across varying levels of sequence coverage.

Entities: Disease

Mesh：

Substances：
DNA

Year: 2008 PMID： 18854868 PMCID： PMC2986170 DOI： 10.1038/ejhg.2008.182

Source DB: PubMed Journal: Eur J Hum Genet ISSN： 1018-4813 Impact factor: 4.246

7 in total

1. dbSNP: the NCBI database of genetic variation.

Authors: S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. Genome sequencing in microfabricated high-density picolitre reactors.

Authors: Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal: Nature Date: 2005-07-31 Impact factor: 49.962

3. Genome-wide in situ exon capture for selective resequencing.

Authors: Emily Hodges; Zhenyu Xuan; Vivekanand Balija; Melissa Kramer; Michael N Molla; Steven W Smith; Christina M Middle; Matthew J Rodesch; Thomas J Albert; Gregory J Hannon; W Richard McCombie
Journal: Nat Genet Date: 2007-11-04 Impact factor: 38.330

4. Direct selection of human genomic loci by microarray hybridization.

Authors: Thomas J Albert; Michael N Molla; Donna M Muzny; Lynne Nazareth; David Wheeler; Xingzhi Song; Todd A Richmond; Chris M Middle; Matthew J Rodesch; Charles J Packard; George M Weinstock; Richard A Gibbs
Journal: Nat Methods Date: 2007-10-14 Impact factor: 28.547

5. Identification of susceptibility loci for cervical carcinoma by genome scan of affected sib-pairs.

Authors: Malin T Engelmark; Emma L Ivansson; Jessica J Magnusson; Inger M Gustavsson; Anna H Beskow; Patrik K E Magnusson; Ulf B Gyllensten
Journal: Hum Mol Genet Date: 2006-10-11 Impact factor: 6.150

6. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

Authors: Fredrik Dahl; Mats Gullberg; Johan Stenberg; Ulf Landegren; Mats Nilsson
Journal: Nucleic Acids Res Date: 2005-04-28 Impact factor: 16.971

7. Accuracy and quality of massively parallel DNA pyrosequencing.

Authors: Susan M Huse; Julie A Huber; Hilary G Morrison; Mitchell L Sogin; David Mark Welch
Journal: Genome Biol Date: 2007 Impact factor: 13.583

7 in total

28 in total

1. Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development.

Authors: Rebecca L Margraf; Jacob D Durtschi; Shale Dames; David C Pattison; Jack E Stephens; Rong Mao; Karl V Voelkerding
Journal: J Biomol Tech Date: 2010-09

2. Design of association studies with pooled or un-pooled next-generation sequencing data.

Authors: Su Yeon Kim; Yingrui Li; Yiran Guo; Ruiqiang Li; Johan Holmkvist; Torben Hansen; Oluf Pedersen; Jun Wang; Rasmus Nielsen
Journal: Genet Epidemiol Date: 2010-07 Impact factor: 2.135

3. Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males.

Authors: Stephen C Collins; Steven M Bray; Joshua A Suhl; David J Cutler; Bradford Coffee; Michael E Zwick; Stephen T Warren
Journal: Am J Med Genet A Date: 2010-10 Impact factor: 2.802

4. Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.

Authors: Ghazal Zaboli; Adam Ameur; Wilmar Igl; Åsa Johansson; Caroline Hayward; Veronique Vitart; Susan Campbell; Lina Zgaga; Ozren Polasek; Gerd Schmitz; Cornelia van Duijn; Ben Oostra; Peter Pramstaller; Andrew Hicks; Tomas Meitinger; Igor Rudan; Alan Wright; James F Wilson; Harry Campbell; Ulf Gyllensten
Journal: Eur J Hum Genet Date: 2011-08-03 Impact factor: 4.246

SNP frequency estimation using massively parallel sequencing of pooled DNA.

1. dbSNP: the NCBI database of genetic variation.

2. Genome sequencing in microfabricated high-density picolitre reactors.

3. Genome-wide in situ exon capture for selective resequencing.

4. Direct selection of human genomic loci by microarray hybridization.

5. Identification of susceptibility loci for cervical carcinoma by genome scan of affected sib-pairs.

6. Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

7. Accuracy and quality of massively parallel DNA pyrosequencing.

1. Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development.

2. Design of association studies with pooled or un-pooled next-generation sequencing data.

3. Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males.

4. Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.

5. A statistical method for the detection of variants from next-generation resequencing of DNA pools.

6. SNP identification, verification, and utility for population genetics in a non-model genus.

7. Identification of rare alleles and their carriers using compressed se(que)nsing.

8. Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region.

9. Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways.

10. Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.