Implementing a biogeographic ancestry inference service for forensic casework.

The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.

Hepatitis C virus in healthy blood donors in Sri Lanka.

INTRODUCTION: Hepatitis C virus (HCV) is the etiological agent for the majority of cases of non-A, non-B hepatitis. As a blood-borne virus, HCV is widely recognized as a major causative agent of post-transfusion non-A, non-B hepatitis. The prevalence of HCV and the distribution of HCV genotypes in Sri Lanka in comparison with the rest of Asia are not well known. MATERIALS AND METHODS: The blood samples collected from healthy blood donors at the National Blood Transfusion Centre of Sri Lanka were screened to determine the prevalence and the genotypes of HCV among blood donors in Sri Lanka. RESULTS: HCV antibodies were found in 53 of 4980 blood donors. However, of the 53 only 8 positive results were confirmed by Reverse Transcription-PCR, which suggests frequent false-positive results or viral clearance. The PCR positive samples were genotyped by DNA sequencing of the Core/E1 regions of HCV genome, and all the HCV viruses belonged to genotype 3, of which 7 were 3a and 1 was 3b. CONCLUSION: HCV is relatively rare among blood donors in Sri Lanka and only genotype 3 was detected in the studied group.

Establishment of a molecular diagnostic system for detecting human papillomavirus in clinical samples in Sri Lanka.

Human papillomavirus (HPV) is associated with variety of clinical conditions that range from innocuous lesions to cancer in both men and women. Consensus primer-mediated PCR assays have enabled screening for a broad spectrum of HPV types. We have established a molecular diagnostic system for detecting HPV DNA in clinical samples from STD clinics in Sri Lanka and compared the efficacy of three different primer sets, MY09/11, GP5+/6+ and CPI/IIG primer sets, to determine which primer set or combination of primers is most efficacious in screening for HPV. Cervical and urethral swabs were obtained from 51 patients who were suspected of having HPV. The presence of HPV DNA in swabs was detected by MY09/11 PCR (33%), GP5+/6+ PCR (72%) and CPI/IIG PCR (57%) primers. HPV DNA was detected in 23% of samples by all three methods, in 43% by any two methods, and in 6% only by GP5+/6+ primer set. GP5+/6+ PCR alone was capable of detecting the most number of HPV positives but, any single PCR method for the detection of HPV may underestimate the true prevalence of HPV in clinical samples. Nested PCR assay with MY09/11 and GP5+/6+ primer sets had higher sensitivity than singleplex PCR but, due to the risk of cross contamination in employing nested PCR, it was concluded that GP5+/6+ PCR is more suitable for HPV DNA detection in epidemiologic and clinical follow-up studies in Sri Lanka.

Haplotype data for 12 Y-chromosome STR loci of Sri Lankans.

Haplotype data estimated from 12 Y-chromosomal STRs were obtained from a sample of 207 unrelated male individuals from Sri Lanka. A total of 195 different haplotypes were identified, of which 183 were unique. Haplotype diversity was found be high (0.9948+/-0.0012) indicating increased discriminating capacity of these 12 Y-STR loci in forensic identification of Sri Lankan individuals. DYS385, representing two loci, was the most diverse marker (0.853). The lowest diversity (0.351) was observed with DYS391.

Genetic profile of 11 autosomal STR loci among the four major ethnic groups in Sri Lanka.

Allele frequencies and statistical parameters of forensic interest are presented for 11 autosomal microsatellites (CSF1PO, TPOX, TH01, D16S539, D13S317, D7S820, F13A, F13B, FESFPS, vWA and LPL) of four ethnic groups in Sri Lanka. A total of 513 unrelated individuals from Sinhalese, Sri Lankan Tamil, Indian Tamil and Sri Lankan Moor population groups were included. Sri Lanka is an island with a multi-ethnic population whose genetic composition has not been previously studied at the ethnic group level. All the 11 microsatellites were found to be highly polymorphic, with the combined power of exclusion being greater than 0.99999, in all four ethnic groups. Overall data analysis suggests that a single combined genetic database could be used for genetic-based identification purposes for the four ethnic groups.

Genotypes of hepatitis C virus (HCV) in liver disease patients in Sri Lanka.

A total of 460 samples (serum or plasma) were obtained from clinically diagnosed liver disease patients from January 2006 to December 2007 and subjected to reverse transcription--polymerase chain reaction (RT-PCR) based detection of HCV. Of these, 32 samples (6.9%) were positive for HCV RNA. Samples that were positive for HCV were genotyped with type specific primers. The genotyping assay was validated by DNA sequencing and phylogenetic analysis. The Sri Lankan isolates were comprised predominantly of genotype 1b (46.9%) followed by genotype 2b (21.9%), 2a (15.6%) and mixed infection with genotypes 1b and 2b (3.1%). This is the first report of the distribution of HCV genotypes in Sri Lanka.

History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation.

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.