Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA

Ranajit Chakraborty, Yixi Zhong, Li Jin, Bruce Budowle

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

We provide experimental evidence showing that, during the restriction- enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, we show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, we derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci.

Original languageEnglish
Pages (from-to)391-401
Number of pages11
JournalAmerican Journal of Human Genetics
Volume55
Issue number2
StatePublished - 11 Aug 1994

Fingerprint

DNA Fingerprinting
Restriction Fragment Length Polymorphisms
Alleles
DNA
Gene Frequency
Databases
Minisatellite Repeats
DNA Restriction Enzymes
Homozygote
Digestion
Gels
Population

Cite this

@article{5f90f70be1cc42a4842a7e99d1bfad28,
title = "Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA",
abstract = "We provide experimental evidence showing that, during the restriction- enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, we show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, we derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci.",
author = "Ranajit Chakraborty and Yixi Zhong and Li Jin and Bruce Budowle",
year = "1994",
month = "8",
day = "11",
language = "English",
volume = "55",
pages = "391--401",
journal = "American Journal of Human Genetics",
issn = "0002-9297",
publisher = "Cell Press",
number = "2",

}

Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA. / Chakraborty, Ranajit; Zhong, Yixi; Jin, Li; Budowle, Bruce.

In: American Journal of Human Genetics, Vol. 55, No. 2, 11.08.1994, p. 391-401.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Nondetectability of restriction fragments and independence of DNA fragment sizes within and between loci in RFLP typing of DNA

AU - Chakraborty, Ranajit

AU - Zhong, Yixi

AU - Jin, Li

AU - Budowle, Bruce

PY - 1994/8/11

Y1 - 1994/8/11

N2 - We provide experimental evidence showing that, during the restriction- enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, we show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, we derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci.

AB - We provide experimental evidence showing that, during the restriction- enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragments are small enough to prevent their reliable sizing on a Southern gel. As a result of such nondetectability of DNA fragments, individuals who show a single-band DNA profile at a VNTR locus may not necessarily be true homozygotes. In a population database, when the presence of such nondetectable alleles is ignored, we show that a pseudodependence of alleles within as well as across loci may occur. Using a known statistical method, under the hypothesis of independence of alleles within loci, we derive an efficient estimate of null allele frequency, which may be subsequently used for testing allelic independence within and across loci. The estimates of null allele frequencies, thus derived, are shown to agree with direct experimental data on the frequencies of HaeIII-null alleles. Incorporation of null alleles into the analysis of the forensic VNTR database suggests that the assumptions of allelic independence within and between loci are appropriate. In contrast, a failure to incorporate the occurrence of null alleles would provide a wrong inference regarding the independence of alleles within and between loci.

UR - http://www.scopus.com/inward/record.url?scp=0028068662&partnerID=8YFLogxK

M3 - Article

C2 - 7913584

AN - SCOPUS:0028068662

VL - 55

SP - 391

EP - 401

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 2

ER -