Literature DB >> 2339707

Theoretical underpinning of the single-molecule-dilution (SMD) method of direct haplotype resolution.

J C Stephens1, J Rogers, G Ruano.   

Abstract

In a recent paper we have shown that DNA haplotypes of multiply heterozygous individuals can be resolved directly by polymerase-chain-reaction (PCR) amplification of a single molecule of genomic template. Our method (the single-molecule-dilution [SMD] method) relies on the stochastic separation of maternal and paternal alleles at high dilution. The stochasticity of separation and the potential for DNA shearing (which could separate the loci of interest) are two factors that can compromise the results of the experiment. This paper explores the consequences of these two factors and shows that the SMD method can be expected to work very reliably even in the presence of a moderate amount of DNA shearing.

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Year:  1990        PMID： 2339707      PMCID： PMC1683843     

Source DB:  PubMed          Journal:  Am J Hum Genet        ISSN： 0002-9297            Impact factor:   11.025


  14 in total

Review 1.  Inference of haplotypes from PCR-amplified samples of diploid populations.

Authors:  A G Clark
Journal:  Mol Biol Evol       Date:  1990-03       Impact factor: 16.240

2.  Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms.

Authors:  J S Wainscoat; A V Hill; A L Boyce; J Flint; M Hernandez; S L Thein; J M Old; J R Lynch; A G Falusi; D J Weatherall
Journal:  Nature       Date:  1986 Feb 6-12       Impact factor: 49.962

3.  Genetic uniformity in two populations of Drosophila melanogaster as revealed by filter hybridization of four-nucleotide-recognizing restriction enzyme digests.

Authors:  M Kreitman; M Aguadé
Journal:  Proc Natl Acad Sci U S A       Date:  1986-05       Impact factor: 11.205

4.  Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers.

Authors:  X F Cui; H H Li; T M Goradia; K Lange; H H Kazazian; D Galas; N Arnheim
Journal:  Proc Natl Acad Sci U S A       Date:  1989-12       Impact factor: 11.205

5.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.

Authors:  R K Saiki; D H Gelfand; S Stoffel; S J Scharf; R Higuchi; G T Horn; K B Mullis; H A Erlich
Journal:  Science       Date:  1988-01-29       Impact factor: 47.728

6.  Biphasic amplification of very dilute DNA samples via 'booster' PCR.

Authors:  G Ruano; W Fenton; K K Kidd
Journal:  Nucleic Acids Res       Date:  1989-07-11       Impact factor: 16.971

7.  Amplification and analysis of DNA sequences in single human sperm and diploid cells.

Authors:  H H Li; U B Gyllensten; X F Cui; R K Saiki; H A Erlich; N Arnheim
Journal:  Nature       Date:  1988-09-29       Impact factor: 49.962

8.  Molecular population genetics of the alcohol dehydrogenase gene region of Drosophila melanogaster.

Authors:  C F Aquadro; S F Desse; M M Bland; C H Langley; C C Laurie-Ahlberg
Journal:  Genetics       Date:  1986-12       Impact factor: 4.562

9.  Restriction-map variation in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Authors:  S W Schaeffer; C F Aquadro; W W Anderson
Journal:  Mol Biol Evol       Date:  1987-05       Impact factor: 16.240

10.  Recombination and balanced chromosome polymorphism suggested by DNA sequences 5' to the human delta-globin gene.

Authors:  N Maeda; J B Bliska; O Smithies
Journal:  Proc Natl Acad Sci U S A       Date:  1983-08       Impact factor: 11.205
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  8 in total

1.  Direct molecular haplotyping of long-range genomic DNA with M1-PCR.

Authors:  Chunming Ding; Charles R Cantor
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-11       Impact factor: 11.205

2.  Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing (CAS).

Authors:  G Ruano; K K Kidd
Journal:  Nucleic Acids Res       Date:  1991-12-25       Impact factor: 16.971

3.  A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations.

Authors:  W Navidi; N Arnheim; M S Waterman
Journal:  Am J Hum Genet       Date:  1992-02       Impact factor: 11.025

4.  Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications.

Authors:  Y M Lo; P Patel; C R Newton; A F Markham; K A Fleming; J S Wainscoat
Journal:  Nucleic Acids Res       Date:  1991-07-11       Impact factor: 16.971

5.  Haplotype of multiple polymorphisms resolved by enzymatic amplification of single DNA molecules.

Authors:  G Ruano; K K Kidd; J C Stephens
Journal:  Proc Natl Acad Sci U S A       Date:  1990-08       Impact factor: 11.205

6.  Understanding the accuracy of statistical haplotype inference with sequence data of known phase.

Authors:  Aida M Andrés; Andrew G Clark; Lawrence Shimmin; Eric Boerwinkle; Charles F Sing; James E Hixson
Journal:  Genet Epidemiol       Date:  2007-11       Impact factor: 2.135

7.  Whole-genome haplotyping by dilution, amplification, and sequencing.

Authors:  Fiona Kaper; Sajani Swamy; Brandy Klotzle; Sarah Munchel; Joseph Cottrell; Marina Bibikova; Han-Yu Chuang; Semyon Kruglyak; Mostafa Ronaghi; Michael A Eberle; Jian-Bing Fan
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-18       Impact factor: 11.205

8.  An efficient method for multi-locus molecular haplotyping.

Authors:  Bernard A Konfortov; Alan T Bankier; Paul H Dear
Journal:  Nucleic Acids Res       Date:  2006-12-07       Impact factor: 16.971
  8 in total

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