Y-chromosomal DNA Research Articles

Mesenchymal stromal cell treatment of donor kidneys during ex vivo normothermic machine perfusion: A porcine renal autotransplantation study.

Normothermic machine perfusion (NMP) of injured kidneys offers the opportunity for interventions to metabolically active organs prior to transplantation. Mesenchymal stromal cells (MSCs) can exert regenerative and anti-inflammatory effects in ischemia-reperfusion injury. The aims of this study were to evaluate the safety and feasibility of MSC treatment of kidneys during NMP using a porcine autotransplantation model, and examine potential MSC treatment-associated kidney improvements up to 14days posttransplant. After 75min of kidney warm ischemia, four experimental groups of n=7 underwent 14h of oxygenated hypothermic machine perfusion. In three groups this was followed by 240min of NMP with infusion of vehicle, 10million porcine, or 10million human adipose-derived MSCs. All kidneys were autotransplanted after contralateral nephrectomy. MSC treatment did not affect perfusion hemodynamics during NMP or cause adverse effects at reperfusion, with 100% animal survival. MSCs did not affect plasma creatinine, glomerular filtration rate, neutrophil gelatinase-associated lipocalin concentrations or kidney damage assessed by histology during the 14days, and MSCs retention was demonstrated in renal cortex. Infusing MSCs during ex vivo NMP of porcine kidneys was safe and feasible. Within the short posttransplant follow-up period, no beneficial effects of ex vivo MSC therapy could be demonstrated.

Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms.

To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.

Large scale follow-up research study: SneakPeek® Early Gender DNA Test 99.9% accurate for fetal sex by live-birth confirmation

Early fetal sex determination has become more prevalent among parents interested in planning for their unborn child. Current advances in non-invasive prenatal testing (NIPT) have facilitated this desire with safe and efficient methods such as the SneakPeek® Early Gender DNA Test (“SneakPeek”). Here, we report the accuracy of SneakPeek® from a large-scale clinical study of 1,029 pregnant women between 7 and 37 weeks of gestation (median =10 weeks). A follow-up survey was conducted on all study participants to determine whether the birth sex of their child matched the fetal sex test result reported by SneakPeek®. Venipuncture blood samples were collected from pregnant women in October through December of 2019, and subsequently analyzed with SneakPeek® to determine fetal sex. After birth, a survey was conducted to obtain live birth information for all participants in the study. Y-chromosome DNA was detected in 505 of the 506 samples from mothers that gave birth to baby boys, providing 99.8% sensitivity. Gender of all 523 newborn girls was identified correctly, resulting in 100% specificity. There were no cases of male DNA contamination identified in this study (i.e. no false positives). In the largest qPCR-based fetal sex test study to date, SneakPeek® test results were confirmed using the gold standard of the baby’s sex at birth. With 99.9% accuracy, SneakPeek® is the most reliable early fetal sex text available for expectant parents

A Franklin expedition officer's burial at Two Grave Bay, King William Island, Nunavut

In 2018, archaeological investigations on King William Island led to the rediscovery of the grave of a member of the 1845 Franklin expedition first recorded in 1879, the exact location of which had been unknown for 139 years. The results of the 2018 investigation confirm the original interpretation that the deceased was a member of the Franklin expedition and a Royal Navy officer. The officer's death likely occurred in late April or early May 1848, during the retreat to the Back River by the expedition's 105 surviving members. Historical and archaeological evidence suggest the integrity of the grave was transformed by at least two temporally distinct episodes and types of disturbance. The officer's identity is unknown, but it is hoped that mitochondrial and Y-chromosome DNA profiles and a digital craniofacial reconstruction will contribute to a future identification.

The Impact of Semen Exposure on the Immune and Microbial Environments of the Female Genital Tract.

Background: Semen induces an immune response at the female genital tract (FGT) to promote conception. It is also the primary vector for HIV transmission to women during condomless sex. Since genital inflammation and immune activation increase HIV susceptibility in women, semen-induced alterations at the FGT may have implications for HIV risk. Here we investigated the impact of semen exposure, as measured by self-reported condom use and Y-chromosome DNA (YcDNA) detection, on biomarkers of female genital inflammation associated with HIV acquisition.Methods: Stored genital specimens were collected biannually (mean 5 visits) from 153 HIV-negative women participating in the CAPRISA 008 tenofovir gel open-label extension trial. YcDNA was detected in cervicovaginal lavage (CVL) pellets by RT-PCR and served as a biomarker of semen exposure within 15 days of genital sampling. Protein concentrations were measured in CVL supernatants by multiplexed ELISA, and the frequency of activated CD4+CCR5+ HIV targets was assessed on cytobrush-derived specimens by flow cytometry. Common sexually transmitted infections (STIs) and bacterial vaginosis (BV)-associated bacteria were measured by PCR. Multivariable linear mixed models were used to assess the relationship between YcDNA detection and biomarkers of inflammation over time.Results: YcDNA was detected at least once in 69% (106/153) of women during the trial (median 2, range 1–5 visits), and was associated with marital status, cohabitation, the frequency of vaginal sex, and Nugent Score. YcDNA detection but not self-reported condom use was associated with elevated concentrations of several cytokines: IL-12p70, IL-10, IFN-γ, IL-13, IP-10, MIG, IL-7, PDGF-BB, SCF, VEGF, β-NGF, and biomarkers of epithelial barrier integrity: MMP-2 and TIMP-4; and with reduced concentrations of IL-18 and MIF. YcDNA detection was not associated with alterations in immune cell frequencies but was related to increased detection of P. bivia (OR = 1.970; CI 1.309–2.965; P = 0.001) at the FGT.Conclusion: YcDNA detection but not self-reported condom use was associated with alterations in cervicovaginal cytokines, BV-associated bacteria, and matrix metalloproteinases, and may have implications for HIV susceptibility in women. This study highlights the discrepancies related to self-reported condom use and the need for routine screening for biomarkers of semen exposure in studies of mucosal immunity to HIV and other STIs.

AYChr-DB: a database of ancient human Y haplogroups.

Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018–2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB—a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.

Genetic evidence suggests a sense of family, parity and conquest in the Xiongnu Iron Age nomads of Mongolia.

In an effort to characterize the people who composed the groups known as the Xiongnu, nuclear and whole mitochondrial DNA data were generated from the skeletal remains of 52 individuals excavated from the Tamir Ulaan Khoshuu (TUK) cemetery in Central Mongolia. This burial site, attributed to the Xiongnu period, was used from the first century BC to the first century AD. Kinship analyses were conducted using autosomal and Y-chromosomal DNA markers along with complete sequences of the mitochondrial genome. These analyses suggested close kin relationships between many individuals. Nineteen such individuals composed a large family spanning five generations. Within this family, we determined that a woman was of especially high status; this is a novel insight into the structure and hierarchy of societies from the Xiongnu period. Moreover, our findings confirmed that the Xiongnu had a strongly admixed mitochondrial and Y-chromosome gene pools and revealed a significant western component in the Xiongnu group studied. Using a fine-scale approach (haplotype instead of haplogroup-level information), we propose Scytho-Siberians as ancestors of the Xiongnu and Huns as their descendants.

Evolution and domestication of the Bovini species.

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull×banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

Reviews of Science for Science Librarians: Direct-to-Consumer DNA Testing for Ancestry as a Complement to Traditional Genealogical Methods

ABSTRACT Almost 100 Million Americans have turned to DTC (Direct-to-Consumer) DNA testing kits to identify their forebears and map the biogeographic areas from which they came. Test results for most Americans of European ancestry are highly accurate and very specific as to homelands. They generally confirm carefully constructed traditional document-search-based genealogies, as is the case with East and Southeast Asian immigrants who maintained in-depth family records owing to traditions of filial piety. For a variety of reasons, traditional genealogical approaches and DTC DNA tests of African Americans cannot yet be as highly specific but developments in testing are very promising. DTC DNA testing of Latinx and Indigenous American (Native Americans) remains somewhat problematic in part due to the very high incidence of admixtures of the two groups, which is further complicated by ethical issues over who is, or is not, a genuine member of any particular tribe. Ancestry-oriented DNA kits continue to rely primarily on SNP (Single-Nucleotide-Polymorphisms), Y-chromosome, and mitochondrial DNA tests, with whole-genome tests still primarily reserved for clinical studies, although more and more kit marketing is now providing information with regard to genetic susceptibility to given diseases or medical conditions.

Y/15 and Y/22 Derivative Chromosomes in Couples with Reproductive Failures: Algorithm of Preimplantation Genetic Testing and Specificity of Inheritance

The present study reports on the results of preimplantation genetic testing and IVF outcomes in four families, where one of the spouses is a carrier of Y/15 or Y/22 derivative chromosome: three cases of male carriers and one—of female carrier. In the cases of male carriers, we detected the predominant inheritance of the derivative chromosomes by the embryos and no abnormalities in sex chromosome segregation. In the case of female carrier, we did not observe either predominant inheritance of derivative chromosome by the embryos or effect of derivative chromosome on sex chromosome segregation. In all families, we revealed a high frequency of embryonic aneuploidies of chromosomes other than those involved in translocation. To exclude inheritance of the derivative chromosome by the offspring, preimplantation genetic testing should be recommended: fluorescent in situ hybridization (FISH), which allows identification of the Y-chromosome satellite DNA, followed by next generation sequencing (NGS) or microarray comparative genomic hybridization (aCGH) to detect other genomic and chromosomal abnormalities.

Trends in Reported Sexual Behavior and Y-Chromosomal DNA Detection Among Female Sex Workers in the Senegal Preexposure Prophylaxis Demonstration Project.

Preexposure prophylaxis (PrEP) can reduce HIV acquisition among female sex workers (FSWs). However, changes in condomless sex frequency after PrEP initiation could reduce PrEP effectiveness when PrEP adherence is suboptimal as well as increase the risk of acquiring other sexually transmitted infections. Objective measures of condomless sex may be more accurate for determining changes in sexual behavior than self-reported measures. We longitudinally measured self-reported condom use, number of clients, and presence of Y-chromosomal DNA (Yc-DNA) in vaginal swabs among 267 FSWs accessing PrEP at 4 clinics in Senegal between 2015 and 2016. We assessed trends in sexual behavior over time since PrEP initiation using generalized estimating equations and evaluated predictors of Yc-DNA detection. We found no increase in self-reported condomless sex with clients (odds ratio [OR], 0.94; 95% confidence interval [CI], 0.89-1.00), main partners (OR, 0.99; 95% CI, 0.96-1.02), or Yc-DNA detection (OR, 0.99; 95% CI, 0.90-1.08) over time since initiation. Y-chromosomal DNA was detected in 34 (22%) of 154 swabs tested and in 15 (26%) of 58 swabs from FSW reporting consistent condom use among both clients and main partners. Self-reported condom use with clients or main partners did not predict Yc-DNA detection. In a FSW PrEP demonstration project in Senegal, we found no evidence of risk compensation among FSWs on PrEP as measured by self-reported behavior or through Yc-DNA detection. Y-chromosomal DNA detection was frequently detected among FSWs reporting consistent condom use, highlighting limitations of self-reported sexual behavioral measures.

Genetic analysis of 27 Y-chromosomal STR loci in a Zimbabwean Shona ethnic group.

Buccal swabs from 200 unrelated Zimbabwean males were collected from voluntary participants located in Harare province. The 5-dye SureID® 27Y Human STR Identification Kit was used to perform multiplex polymerase chain reactions (PCR) and generate Y-chromosomal DNA profiles. This kit targets markers DYS456, DYS576, DYS570, DYS481, DYF387S1, DYS627, DYS393, DYS391, DYS390, DYS635, DYS449, DYS533, DYS438, DYS389I, DYS448, DYS389II, DYS19, GATA_H4, DYS518, DYS458, DYS460, DYS437, DYS439, DYS392, and DYS385, similar to the Yfiler® Plus Amplification Kit. A total of 161 haplotypes were generated with the PowerPlex® Y system, whereas 159 complete haplotypes were generated for the Yfiler® Plus system. Haplotype Discrimination Capacity (DC) with the Yfiler® Plus system was determined to be 0.9686, while the Genetic Diversity (GD) of the targeted loci ranged from 0.03748 at DYS392 to 0.867239 at DYS449. One haplotype contained the triallelic pattern 37, 38, and 39 at DYS387S1. In addition, marker DYS387S1 and marker DYS385 had 13 counts of microvariant alleles overall, while 9 null allele counts were noted at marker DYS448. Genetic distances between our population data and 22 other data sets from African countries and people of African descent were estimated and results showed significant genetic variation.

Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic

BackgroundHelicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human.MethodsWe examined both H. pylori DNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from cultured H. pylori were analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses.ResultsH. pylori strains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both in H. pylori and in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant in H. pylori infection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) of H. pylori was not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent.ConclusionsGenetic features of H. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy between H. pylori and the host human genotypes support the hypothesis that adaptability of hspAmerind H. pylori strains are weaker than hpEurope strains. H. pylori strains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.

PrEP Use Among Female Sex Workers: No Evidence for Risk Compensation.

Little is known about risk compensation among female sex workers (FSW) on HIV pre-exposure prophylaxis (PrEP), and self-report of sexual behaviors is subject to bias. Prospective observational PrEP demonstration study conducted among FSW in Cotonou, Benin. Over a period of 24 months, we assessed and compared trends in unprotected sex as measured by self-report (last 2 or 14 days), by detection of sexually transmitted infections (STIs), and by vaginal detection of prostate-specific antigen and Y-chromosomal DNA, 2 biomarkers of semen exposure in the last 2 or 14 days, respectively. Trends were assessed and compared using a log-binomial regression that was simultaneously fit for all unprotected sex measures. Of 255 participants, 120 (47.1%) completed their follow-up. Prevalence of STI decreased from 15.8% (95% confidence interval: 11.8% to 21.0%) at baseline to 2.1% (95% confidence interval: 0.4% to 10.2%) at 24 months of follow-up (P-trend = 0.04). However, we observed no trend in self-report of unprotected sex in the last 2 (P = 0.42) or 14 days (P = 0.49), nor in prostate-specific antigen (P = 0.53) or Y chromosomal DNA (P = 0.25) over the same period. We observed no statistically significant difference between trends in self-report of unprotected sex and trends in biomarkers of semen exposure in the last 2 days (P = 0.14) or in the last 14 days (P = 0.29). We observed no evidence of risk compensation, and a decrease in STI among FSW on PrEP. PrEP intervention may be an opportunity to control STI among FSW. Future studies should assess risk compensation with biomarkers of semen exposure when possible.

Daily Vaginal Swabs and Mobile Phone Sex Report for Assessing HIV Virion Exposure Prospectively Among a Cohort of Young Sexually Active Women in South Africa (HVTN 915).

Measurements of HIV exposure could help identify subpopulations at highest risk of acquisition and improve the design of HIV prevention efficacy trials and public health interventions. The HVTN 915 study evaluated the feasibility of self-administered vaginal swabs for detection of HIV virions to assess exposure. Fifty 18- to 25-year-old sexually active HIV-seronegative women using contraception were enrolled in Soweto, South Africa. Participants self-administered daily vaginal swabs and answered sexual behavior questions through mobile phone for 90 days. Clinician-administered vaginal swabs, behavioral questionnaires, HIV diagnostic testing, and counseling were performed at 8 clinic visits. Glycogen concentrations assessed adherence to swabbing. Y-chromosome DNA (Yc-DNA) assessed the accuracy of reported condom use. HIV exposure was measured by virion polymerase chain reaction in swabs from 41 women who reported unprotected vaginal sex during follow-up. Glycogen was detected in 315/336 (93.8%) participant-collected and in all clinician-collected swabs. Approximately 20/39 daily swabs (51.3%) linked to mobile reports of unprotected sex tested positive for Yc-DNA, whereas 10/187 swabs collected after 3 days of abstinence or protected sex (5.3%) had detectable Yc-DNA. No participant became HIV infected during the study; yet, exposure to HIV was detected by nucleic acids in 2 vaginal swabs from 1 participant, collected less than 1 hour after coitus. There was high adherence to daily vaginal swabbing. Daily mobile surveys had accurate reporting of unprotected sex. Detection of HIV in self-collected vaginal swabs from an uninfected participant demonstrated it was possible to measure HIV exposure, but the detection rate was lower than expected.

Обзор результатов начального этапа палеогенетических исследований населения эпохи бронзы Минусинских котловин

The article presents the review of the results of paleogenetic studies conducted by various research groups using materials from the funerary sites of the Bronze Age of the Minusinsk Hollow (south of the Krasnoyarsk Territory and the Republic of Khakassia) and analyzes the results obtained by comparing the complete genome of the ancient man and the data of phylogenetically informative markers (mtDNA and Y-chromosome DNA). As a result, it was established that in the Bronze Age in the territory of the Middle Yenisei there was a regular change of population, which indicates a high migration activity. The formation of archaeological cultures of this period (Afanasyevskaya, Okunevskaya, Andronovskaya) began with the appearance of a large group of new people, almost completely crowding out their predecessors. Evidence of the assimilation of local residents into new cultural formations is rare and not systemic. The most difficult situation is with the sites of the Late Bronze period due to the small number of tests carried out so far.

Kashmiris phylogenetic depictions through uniparental and biparental genetic markers.

In this study, the Kashmiri population was genetically screened for fifteen autosomal STRs, seventeen Y-chromosomal STRs and mitochondrial DNA control region SNPs. Autosomal STRs exhibited that D2S1338 was the most discriminatory locus with value of 0.963 whereas combine power of discrimination was 0.999999999999999. On the other hand, analysis of Y-chromosomal STRs generated 59 distinct haplotypes of which 52 were unique with haplotype diversity value of 0.99752. Mitochondrial D-loop analysis resulted that haplogroups M and U were found most prevalent with 25% each. Haplotypic data of Y-STRs was submitted to YHRD under accession number YA004153 whereas mitochondrial DNA control region (CR) sequences were submitted to EMPOP with accession number EMP00683.

Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing

Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the “minimal reference phylogeny for the human Y chromosome” (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man’s paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required.

Application of embryo biopsy and sex determination via polymerase chain reaction in a commercial equine embryo transfer program in Argentina.

Embryo biopsy for fetal sexing has clinical application, but few reports are available of its use within an active embryo transfer program. We evaluated results on biopsy of 459 embryos over one breeding season. There were no significant differences in pregnancy rate between biopsied and non-biopsied embryos (72% vs 73%) or for biopsied embryos recovered at the centre (73%) compared with those shipped overnight (72%). However, the pregnancy rate decreased significantly in shipped embryos biopsied ≥20h after collection. Overall, 86% of biopsies provided a sex diagnosis. The likelihood of a positive genomic (g) DNA result was significantly higher for biopsies from large blastocysts (96%) than from smaller embryos (70-85%). In total, 38% of biopsies were positive for Y chromosome DNA (Y-DNA) and were diagnosed as male. Subsequently, 95% of Y-DNA-positive embryos were confirmed as male and 78% of Y-DNA-negative embryos were confirmed as female. The accuracy of prediction of female (Y-DNA negative) was significantly higher when the biopsy sample was probed for Y-DNA only compared with probing for both gDNA and Y-DNA. We estimate that by transferring only Y-DNA-negative embryos, 3% of potential female pregnancies may have been lost, and production of male pregnancies was reduced by 72%.

A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.