R. Chakraborty et al., NONDETECTABILITY OF RESTRICTION FRAGMENTS AND INDEPENDENCE OF DNA FRAGMENT SIZES WITHIN AND BETWEEN LOCI IN RFLP TYPING OF DNA, American journal of human genetics, 55(2), 1994, pp. 391-401
We provide experimental evidence showing that, during the restriction-
enzyme digestion of DNA samples, some of the HaeIII-digested DNA fragm
ents are small enough to prevent their reliable sizing on a Southern g
el. As a result of such nondetectability of DNA fragments, individuals
who show a single-band DNA profile at a VNTR locus may not necessaril
y 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 sta
tistical method, under the hypothesis of independence of alleles withi
n loci, we derive an efficient estimate of null allele frequency, whic
h 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 betwe
en loci.