Genome Amplification of Single Sperm Using Multiple Displacement Amplification

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jun 9

PMID 15942023

Citations 23

Authors

Zhengwen Jiang

Xingqi Zhang

Ranjan Deka

Li Jin

Affiliations

Soon will be listed here.

Abstract

Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.

Citing Articles

Conventional IVF is feasible in preimplantation genetic testing for aneuploidy.

Zhang S, Xie P, Lan F, Yao Y, Ma S, Hu L J Assist Reprod Genet. 2023; 40(10):2333-2342.

PMID: 37656381 PMC: 10504148. DOI: 10.1007/s10815-023-02916-7.

Recent advances and application of whole genome amplification in molecular diagnosis and medicine.

Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X MedComm (2020). 2022; 3(1):e116.

PMID: 35281794 PMC: 8906466. DOI: 10.1002/mco2.116.

Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA.

Andresen I, Orr R, Krabberod A, Shalchian-Tabrizi K, Brate J Sci Rep. 2021; 11(1):12820.

PMID: 34140556 PMC: 8211769. DOI: 10.1038/s41598-021-92092-4.

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis.

Lopez-Escardo D, Grau-Bove X, Guillaumet-Adkins A, Gut M, Sieracki M, Ruiz-Trillo I Sci Rep. 2017; 7(1):11025.

PMID: 28887541 PMC: 5591225. DOI: 10.1038/s41598-017-11466-9.

Increasing amplification success of forensic DNA samples using multiple displacement amplification.

Ballantyne K, van Oorschot R, Mitchell R Forensic Sci Med Pathol. 2015; 3(3):182-7.

PMID: 25869161 DOI: 10.1007/s12024-007-0017-2.

References

Wiehe T, Mountain J, Parham P, Slatkin M . Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns. Genet Res. 2000; 75(1):61-73. DOI: 10.1017/s0016672399004036. View

Wang G, Maher E, Brennan C, Chin L, Leo C, Kaur M . DNA amplification method tolerant to sample degradation. Genome Res. 2004; 14(11):2357-66. PMC: 525695. DOI: 10.1101/gr.2813404. View

Carter K, Robertson B, Kempenaers B . A differential DNA extraction method for sperm on the perivitelline membrane of avian eggs. Mol Ecol. 2000; 9(12):2149-50. DOI: 10.1046/j.1365-294x.2000.01114.x. View

Viguera E, Canceill D, Ehrlich S . In vitro replication slippage by DNA polymerases from thermophilic organisms. J Mol Biol. 2001; 312(2):323-33. DOI: 10.1006/jmbi.2001.4943. View

Goldstein D . Islands of linkage disequilibrium. Nat Genet. 2001; 29(2):109-11. DOI: 10.1038/ng1001-109. View

Jeffreys A, Kauppi L, Neumann R . Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet. 2001; 29(2):217-22. DOI: 10.1038/ng1001-217. View

Daly M, Rioux J, Schaffner S, Hudson T, Lander E . High-resolution haplotype structure in the human genome. Nat Genet. 2001; 29(2):229-32. DOI: 10.1038/ng1001-229. View

Schneider J, Peto T, Boone R, Boyce A, Clegg J . Direct measurement of the male recombination fraction in the human beta-globin hot spot. Hum Mol Genet. 2002; 11(3):207-15. DOI: 10.1093/hmg/11.3.207. 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

10.

Gabriel S, Schaffner S, Nguyen H, Moore J, Roy J, Blumenstiel B . The structure of haplotype blocks in the human genome. Science. 2002; 296(5576):2225-9. DOI: 10.1126/science.1069424. View

11.

Hubert R, MacDonald M, Gusella J, Arnheim N . High resolution localization of recombination hot spots using sperm typing. Nat Genet. 1994; 7(3):420-4. DOI: 10.1038/ng0794-420. View

12.

Zangenberg G, Huang M, Arnheim N, Erlich H . New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm. Nat Genet. 1995; 10(4):407-14. DOI: 10.1038/ng0895-407. View

13.

Cheung V, Nelson S . Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc Natl Acad Sci U S A. 1996; 93(25):14676-9. PMC: 26194. DOI: 10.1073/pnas.93.25.14676. View

14.

Jeffreys A, Murray J, Neumann R . High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol Cell. 1998; 2(2):267-73. DOI: 10.1016/s1097-2765(00)80138-0. View

15.

Wells D, Sherlock J, Handyside A, Delhanty J . Detailed chromosomal and molecular genetic analysis of single cells by whole genome amplification and comparative genomic hybridisation. Nucleic Acids Res. 1999; 27(4):1214-8. PMC: 148305. DOI: 10.1093/nar/27.4.1214. View

16.

Girardet A, Lien S, Leeflang E, Beaufrere L, Tuffery S, Munier F . Direct estimation of the recombination frequency between the RB1 gene and two closely linked microsatellites using sperm typing. Eur J Hum Genet. 1999; 7(2):239-42. DOI: 10.1038/sj.ejhg.5200250. View

17.

Klein C, Schardt J, Pantel K, Speicher M, Riethmuller G . Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A. 1999; 96(8):4494-9. PMC: 16360. DOI: 10.1073/pnas.96.8.4494. View

18.

Park C, Frank M, Lewin H . Fine-mapping of a region of variation in recombination rate on BTA23 to the D23S22-D23S23 interval using sperm typing and meiotic breakpoint analysis. Genomics. 1999; 59(2):143-9. DOI: 10.1006/geno.1999.5869. View

19.

Canceill D, Viguera E, Ehrlich S . Replication slippage of different DNA polymerases is inversely related to their strand displacement efficiency. J Biol Chem. 1999; 274(39):27481-90. DOI: 10.1074/jbc.274.39.27481. View

20.

May C, Shone A, Kalaydjieva L, Sajantila A, Jeffreys A . Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOX. Nat Genet. 2002; 31(3):272-5. DOI: 10.1038/ng918. View