Martin Tracey

Microvariation at the human D1S80 locus.

Abstract The minisatellite locus D1S80, (location: 1p35– p36), GenBank sequence accession # D28507), is a variable number of tandem repeat (VNTR) locus with a 16 base pair repeat size. The sequence of the predominant core repeat region and variants of the D1S80 locus were determined to ascertain whether sequence variation or size variation is the cause of altered migration of some D1S80 alleles. A total of 23 alleles from 14 individuals, previously typed based on the number of repeats (i.e. nominal alleles) for the D1S80 locus, were selected for sequence analysis. The individuals were from African American, Caucasian, and Hispanic databases. From these, 18 different repeat unit sequences were observed and arbitrarily designated A–R. Structural relationships between the alleles became more apparent when the arrays of repeat units were divided into common motifs or super-repeat domains. Six motifs ranging from 3 to 9 repeat units were identified. Several of the alleles included repeat arrays which were too diverse to predict an evolutionary relationship, however, there are two general repeat motif arrays and each has some relationship with either the 18 or the 24 repeat allele. The D1S80 allelic polymorphism is primarily due to variation in the number of repeat units and to sequence variation among repeats, however, it can not be ruled out that some rare alleles may be due to insertions or deletions.

Allele Frequencies of 13 STR Loci and the D1S80 Locus in a Tamil Population from Madras, India

Allele Frequencies of 13 STR Loci and the D1S80 Locus in a Tamil Population from Madras, India

DNA fingerprinting: Basic techniques, problems, and solutions

Abstract The series of techniques and procedures commonly known as “DNA fingerprinting” is gaining acceptance among members of the legal profession. This article reviews the current state of this young science by outlining the scientific protocols and the nature of the mathematical calculations leading to the exclusion or inclusion of individuals in legal matters. In addition, some of the problems inherent in DNA fingerprinting as it is currently done are discussed. Technologies and ideas that will improve the current situation are presented, and areas in need of further basic research are identified.

Y chromosome STR allelic and haplotype diversity in five ethnic Tamil populations from Tamil Nadu, India

We have analyzed 17 Y chromosomal STR loci in a population sample of 154 unrelated male individuals of the Tamil ethnic group residing in the state of Tamil Nadu, Southern India using AmpFlSTR(R) Yfiler PCR amplification kit. The population samples consist of the following castes: Kongu Gounder (KOG), Nadar Hindu (NAH), Agamudayar (AGA), Parayar (PAR) and other Tamil individuals (MCT) of mixed castes. A total of 152 unique haplotypes were identified among the 154 individuals studied. The haplotype diversity was found to be 0.9935 or higher for all the five groups. The results of population pairwise Fst p values indicate no statistically significant differentiation between the five populations in this study, but the results were highly significant when compared with 12 other global populations (p<0.05). Comparison of populations in this study with other national and global populations using Principal co-ordinate analysis (PCA) using Rst distance matrix indicates a delineation of all the Indian populations from other unrelated populations.

Genetic variation of 15 autosomal microsatellite loci in a Tamil population from Tamil Nadu, Southern India

The genetic profiles for 15 autosomal microsatellite loci were analyzed in a Tamil population from Southern India to study the genetic diversities and relatedness of this population with other national and global populations. Statistical analyses of the data revealed all loci were within Hardy-Weinberg Equilibrium (HWE) expectations with the exception of the locus D5S818 (p=0.011). A significantly greater inter-individual variation (Fst=99%) observed within the individuals among the four subgroups in this study and low population differentiation (Fst=1%) suggests relative genetic closeness of these four subgroups. This indicates that the populations in the southern region of India might have a common ancestry or probably experienced high gene flow during the period of their coexistence. The Neighbor Joining tree derived from genetic distances of samples from this study and other national and global populations show clustering of all the Indian populations in one branch of the tree while the African and Middle Eastern populations cluster in a separate branch. Principal Co-ordinate Analysis of the genetic distance data show clustering similar to the NJ tree.

Assessing the Risk of Secondary Transfer Via Fingerprint Brush Contamination Using Enhanced Sensitivity DNA Analysis Methods.

Experiments were performed to determine the extent of cross‐contamination of DNA resulting from secondary transfer due to fingerprint brushes used on multiple items of evidence. Analysis of both standard and low copy number (LCN) STR was performed. Two different procedures were used to enhance sensitivity, post‐PCR cleanup and increased cycle number. Under standard STR typing procedures, some additional alleles were produced that were not present in the controls or blanks; however, there was insufficient data to include the contaminant donor as a contributor. Inclusion of the contaminant donor did occur for one sample using post‐PCR cleanup. Detection of the contaminant donor occurred for every replicate of the 31 cycle amplifications; however, using LCN interpretation recommendations for consensus profiles, only one sample would include the contaminant donor. Our results indicate that detection of secondary transfer of DNA can occur through fingerprint brush contamination and is enhanced using LCN‐DNA methods.

Investigating SNPs Flanking the D1S80 Locus in a Tamil Population from India

Abstract D1S80 is a 16-bp variable number of tandem repeats minisatellite. We analyzed single nucleotide polymorphisms (SNPs) flanking this locus in a Tamil population. Alleles ranged from 15 through 41 repeats, with alleles 18 and 24 being predominant with frequencies of 31% and 34.5%, respectively, suggesting a bimodal allelic distribution. All the 18-repeat alleles are associated with HinfI(+) and FnuAHI(-) restriction site polymorphisms at the 5′ and 3′ ends, respectively. Allele 24 is associated with HinfI(-) and Fnu4HI(+). Of the alleles tested, 98.5% have a linkage of two specific SNP polymorphisms. If an allele is positive for HinfI, then it is negative for Fnu4HI, and if an allele is negative for HinfI, it is then positive for Fnu4HI, which demonstrates strong linkage disequilibrium between the two polymorphic SNPs. This suggests that reciprocal crossover is not involved in changes in the number of repeats, as few exchanges are seen in the flanking regions. The repeat allele-SNP association might be involved with the internal structure of the locus micropolymorphisms, possibly a double-strand break hotspot.

Comparison of VNTR allele frequencies and inclusion probabilities over six populations

There is considerable debate about the methodologies used to estimate VNTR (Variable Number of Tandem Repeats) multi-locus genotype frequencies or odds of inclusion in forensic cases. To compare two of the methods in use, allele frequency distributions among six populations were compared and the effect of population heterogeneity on VNTR multi-locus genotype frequency estimation was examined. Genotype frequencies estimated from single population data were one or two orders of magnitude smaller than those estimated by picking the highest allele frequency in a group of subpopulations to estimate genotype frequencies using a ceiling principle. The average change does not appear to be very sensitive to the set of subpopulations used; four locus frequencies still give inclusion odds of one in a million or less. We think that use of the ceiling principle solves both the statistical problem engendered by subpopulation heterogeneity and the legal problem of assuming that the prepetrator and suspect belong to the same subpopulation. The counterintuitive fact of human genetic polymorphism is that it is easier to identify an individual than it is to identify the subpopulation, ethnic group or race to which that individual belongs.

Mutation at the Human D1S80 Minisatellite Locus

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of 1.04 × 10−4 and a female mutation rate of 5.18 × 10−5 with an overall mutation rate of approximately 7.77 × 10−5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.