Two Methods of Whole-genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel

Overview

Journal Genome Res

Specialty Genetics

Date 2004 May 5

PMID 15123587

Citations 61

Authors

David L Barker

Mark S T Hansen

A Fawad Faruqi

Diane Giannola

Orlando R Irsula

Roger S Lasken

Martin Latterich

Vladimir Makarov

Arnold Oliphant

Jonathon H Pinter

Richard Shen

Irina Sleptsova

William Ziehler

Eric Lai

Affiliations

Soon will be listed here.

Abstract

Comprehensive genome scans involving many thousands of SNP assays will require significant amounts of genomic DNA from each sample. We report two successful methods for amplifying whole-genomic DNA prior to SNP analysis, multiple displacement amplification, and OmniPlex technology. We determined the coverage of amplification by analyzing a SNP linkage marker set that contained 2320 SNP markers spread across the genome at an average distance of 2.5 cM. We observed a concordance of >99.8% in genotyping results from genomic DNA and amplified DNA, strongly indicating the ability of both methods used to amplify genomic DNA in a highly representative manner. Furthermore, we were able to achieve a SNP call rate of >98% in both genomic and amplified DNA. The combination of whole-genome amplification and comprehensive SNP linkage analysis offers new opportunities for genetic analysis in clinical trials, disease association studies, and archiving of DNA samples.

Citing Articles

ddRAD Sequencing and DNA Barcoding.

Ivanov V, Lee K, Mutanen M Methods Mol Biol. 2024; 2744:213-221.

PMID: 38683321 DOI: 10.1007/978-1-0716-3581-0_13.

Embryo biopsies for genomic selection in tropical dairy cattle.

Oliveira C, Camargo L, Silva M, Saraiva N, Quintao C, Machado M Anim Reprod. 2023; 20(2):e20230064.

PMID: 37547565 PMC: 10399131. DOI: 10.1590/1984-3143-AR2023-0064.

Determination of Pleiotropic Effect of Warfarin in and Genotypes in Patients With Heart Valve Replacement.

Shafique H, Ashraf N, Rashid A, Majeed A, Afsar T, Daly A Front Cardiovasc Med. 2022; 9:895169.

PMID: 35757332 PMC: 9226342. DOI: 10.3389/fcvm.2022.895169.

Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae).

Ivanov V, Marusik Y, Petillon J, Mutanen M Sci Rep. 2021; 11(1):2177.

PMID: 33500478 PMC: 7838170. DOI: 10.1038/s41598-021-81788-2.

Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, ).

Cruaud A, Groussier G, Genson G, Saune L, Polaszek A, Rasplus J PeerJ. 2018; 6:e5640.

PMID: 30356952 PMC: 6195110. DOI: 10.7717/peerj.5640.

References

Wang V, Bell D, Berkowitz R, Mok S . Whole genome amplification and high-throughput allelotyping identified five distinct deletion regions on chromosomes 5 and 6 in microdissected early-stage ovarian tumors. Cancer Res. 2001; 61(10):4169-74. View

Lizardi P, Huang X, Zhu Z, Thomas D, Ward D . Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet. 1998; 19(3):225-32. DOI: 10.1038/898. View

Hijikata M, Mishiro S, Miyamoto C, Furuichi Y, Hashimoto M, Ohta Y . Genetic polymorphism of the MxA gene promoter and interferon responsiveness of hepatitis C patients: revisited by analyzing two SNP sites (-123 and -88) in vivo and in vitro. Intervirology. 2002; 44(6):379-82. DOI: 10.1159/000050075. View

Dean F, Hosono S, Fang L, Wu X, Faruqi A, Bray-Ward P . Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A. 2002; 99(8):5261-6. PMC: 122757. DOI: 10.1073/pnas.082089499. View

Oliphant A, Barker D, Stuelpnagel J, Chee M . BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques. 2002; Suppl:56-8, 60-1. View

Roses A . Genome-based pharmacogenetics and the pharmaceutical industry. Nat Rev Drug Discov. 2002; 1(7):541-9. DOI: 10.1038/nrd840. View

Langmore J . Rubicon Genomics, Inc. Pharmacogenomics. 2002; 3(4):557-60. DOI: 10.1517/14622416.3.4.557. View

Zhou X, Tan F, Reveille J, Wallis D, Milewicz D, Ahn C . Association of novel polymorphisms with the expression of SPARC in normal fibroblasts and with susceptibility to scleroderma. Arthritis Rheum. 2002; 46(11):2990-9. DOI: 10.1002/art.10601. View

Buckley P, Mantripragada K, Benetkiewicz M, Tapia-Paez I, Diaz De Stahl T, Rosenquist M . A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet. 2002; 11(25):3221-9. DOI: 10.1093/hmg/11.25.3221. View

10.

Li P, Wood T, Thompson J . Diversity of mutations and distribution of single nucleotide polymorphic alleles in the human alpha-L-iduronidase (IDUA) gene. Genet Med. 2003; 4(6):420-6. DOI: 10.1097/00125817-200211000-00004. View

11.

Smith J, James D, Dansky H, Wittkowski K, Moore K, Breslow J . In silico quantitative trait locus map for atherosclerosis susceptibility in apolipoprotein E-deficient mice. Arterioscler Thromb Vasc Biol. 2003; 23(1):117-22. DOI: 10.1161/01.atv.0000047461.18902.80. View

12.

Lage J, Leamon J, Pejovic T, Hamann S, Lacey M, Dillon D . Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res. 2003; 13(2):294-307. PMC: 420367. DOI: 10.1101/gr.377203. View

13.

Wang J, Hegele R . Genomic basis of cystathioninuria (MIM 219500) revealed by multiple mutations in cystathionine gamma-lyase (CTH). Hum Genet. 2003; 112(4):404-8. DOI: 10.1007/s00439-003-0906-8. View

14.

Hosono S, Faruqi A, Dean F, Du Y, Sun Z, Wu X . Unbiased whole-genome amplification directly from clinical samples. Genome Res. 2003; 13(5):954-64. PMC: 430878. DOI: 10.1101/gr.816903. View

15.

Lovmar L, Fredriksson M, Liljedahl U, Sigurdsson S, Syvanen A . Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res. 2003; 31(21):e129. PMC: 275486. DOI: 10.1093/nar/gng129. View

16.

Gribble S, Ng B, Prigmore E, Burford D, Carter N . Chromosome paints from single copies of chromosomes. Chromosome Res. 2004; 12(2):143-51. DOI: 10.1023/b:chro.0000013167.12527.f0. View

17.

Gunderson K, Kruglyak S, Graige M, Garcia F, Kermani B, Zhao C . Decoding randomly ordered DNA arrays. Genome Res. 2004; 14(5):870-7. PMC: 479114. DOI: 10.1101/gr.2255804. View

18.

Fan J, Oliphant A, Shen R, Kermani B, Garcia F, Gunderson K . Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol. 2004; 68:69-78. DOI: 10.1101/sqb.2003.68.69. View

19.

Zhang L, Cui X, Schmitt K, Hubert R, Navidi W, Arnheim N . Whole genome amplification from a single cell: implications for genetic analysis. Proc Natl Acad Sci U S A. 1992; 89(13):5847-51. PMC: 49394. DOI: 10.1073/pnas.89.13.5847. View

20.

Telenius H, Carter N, Bebb C, Nordenskjold M, Ponder B, Tunnacliffe A . Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992; 13(3):718-25. DOI: 10.1016/0888-7543(92)90147-k. View