Human sample authentication in biomedical research: comparison of two platforms

Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.

Development and validation of a multiplex 19 X-chromosomal short tandem repeats typing system for forensic purposes

X-chromosome short tandem repeat (X-STR) markers are a powerful complementary system used for paternity and forensic casework. This study presents the development and validation of a new highly efficient multiplex-fluorescent-labeled 19 X-STR typing system, including DXS10079, DXS101, DXS10135, DXS10162, DXS6795, DXS6800, DXS6803, DXS6807, DXS6809, DXS6810, DXS7133, DXS7423, DXS981, DXS9902, DXS9907, GATA165B12, GATA172D05, GATA31E08 and HPRTB along with sex-typing locus, amelogenin. The system was validated according to guidelines issued by the Scientific Working Group on DNA Analysis Methods. Allele frequency and forensic parameters were investigated from 1085 (494 males and 591 females) unrelated Beijing Han individuals, the combined power of discrimination by the 19 X-STR loci in females and males, as well as the combined mean exclusion chance in trios and duos, were 0.999999999999999995, 0.99999999995, 0.9999999995, and 0.9999996, respectively. The results demonstrate that this multiplex system is robust and reliable, and considered to be a powerful tool for forensic application.

“This Gig Is Not for Women”: Gender Stereotyping in Online Hiring

This study examines gender segregation in the context of the so-called gig economy. In particular, it explores the role that stereotypes about male and female occupations play in sorting men and women into different jobs in an online freelance marketplace. The findings suggest that gender stereotypes are particularly salient in online hiring because employers typically contract for short-term, relatively low-value jobs based on limited information about job applicants. These conditions trigger the use of cognitive shortcuts about intrinsic gender characteristics linked to different skills and occupations. The results corroborate that female candidates are less likely to be hired for male-typed jobs (e.g., software development) but more likely to be hired for female-typed jobs (e.g., writing and translation) than equally qualified male candidates. Further, the study investigates three mechanisms predicted to attenuate the female penalty in male-typed jobs. The penalty is found to be self-reinforcing, as it perpetuates gender imbalances in worker activity across job categories that strengthen the sex typing of occupations.

Microsatellite characterisation and sex-typing in two invasive parakeet species, the monk parakeet Myiopsitta monachus and ring-necked parakeet Psittacula krameri

Invasive species can have wide-ranging negative impacts, and an understanding of the process and success of invasions can be vital to determine management strategies, mitigate impacts and predict range expansions of such species. Monk parakeets (Myiopsitta monachus) and ring-necked parakeets (Psittacula krameri) are both widespread invasive species, but there has been little research into the genetic and social structure of these two species despite the potential links with invasion success. The aim of this study was to isolate novel microsatellite loci from the monk parakeet and characterise them in both monk and ring-necked parakeets in order to facilitate future investigations into their behaviour and population ecology. Sex-typing markers were also tested in both species. Of the 20 microsatellite loci assessed in 24 unrelated monk parakeets, 16 successfully amplified and were polymorphic displaying between 2 and 14 alleles (mean = 8.06). Expected heterozygosity ranged from 0.43 to 0.93 and observed heterozygosity ranged from 0.23 to 0.96. Nine of the 20 loci also successfully amplified and were polymorphic in the ring-necked parakeet, displaying between 2 and 10 alleles. Suitable markers to sex both species and a Z-linked microsatellite locus were identified. A multiplex marker set was validated for monk parakeets. These novel microsatellite loci will facilitate fine and broad-scale population genetic analyses of these two widespread invasive species.

Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y

Background Since the early days of PCR techniques, sex identification, “sex-typing,” of genomic DNA samples has been a fundamental part of human forensic analysis but also in animal genetics aiming at strategic livestock breeding. Most analyses are employing the AMELX/AMELY gene loci on the X and Y chromosomes present in most mammals. We hypothesize that sex-typing in humans is also possible based on the genes NLGN4X and NLGN4Y, which represent X and Y chromosome-specific copies of a common ancestral neuroligin-4 orthologue. Methods Genomic DNA was isolated from human blood and buccal cell samples (total n = 111) and submitted to two different strategies: (a) a traditional two-primer PCR approach detecting an insertion/deletion (indel) polymorphism immediately upstream of the translational start on exon 1 and (b) detection of a single nucleotide polymorphism, SNP, on the translational stop carrying exon 7. The SNP detection was based on a quantitative PCR approach (rhAMP genotyping) employing DNA/RNA hybrid oligonucleotides that were blocked and which could only be activated upon perfect annealing to the target DNA sequence. Results All indel PCR-tested human DNA samples showed two bands for males representing X- and Y-specific copies of NLGN4 and a single band for female samples, i.e., homozygosity of NLGN4X and absence of NLGN4Y, in accordance with the self-reported sex of the donors. These results were in perfect agreement with the results of the rhAMP-based SNP-detection method: all males were consequently positive for both alleles, representing either SNP variant, and females were interpreted as homozygous regarding the SNP variant found in NLGN4X. Both methods have shown reliable and consistent results that enabled us to infer the sex of donor DNA samples across different ethnicities. Conclusions These results indicate that the detection of human NLGN4X/Y is a suitable alternative to previously reported methods employing gene loci such as AMELX/Y. Furthermore, this is the first report applying successfully the rhAMP-genotyping strategy as a means for SNP-based sex-typing, which consequently will be applicable to other gene loci or different species as well.

Grieving those Who Still Live: Loss Experienced by Parents of Transgender Children

Transgender identity can be defined as the self-awareness of a discrepancy between the assigned sex at birth and the personal gender identity of an individual. This study assumed the constructionist perspective, focused on the influence of culture on sex-typing and the representations of gender in child development. This research considers how parents of transgender children emotionally handled the transition. Being faced with a child’s transgender identity may cause an emotional experience similar to mourning, in particular, ambiguous loss (Coolhart, Ritenour & Grodzinski 2018, McGuire et al. 2016, Norwood 2013). In this qualitative research, 97 associations dealing with Gay, Lesbian, Bisexual and Transgender (GLBT) issues were contacted to recruit participants from three different countries: Italy, Spain and U.S.A. The sample includes 18 parents of trangender people who completed an ad hoc questionnaire. A brief standard story was constructed about an experience of sexual transition, followed by some questions on the experience of parental mourning during the transgender transition of their children. The corpora were analysed in the three original languages, and the analysis was performed with Atlas.ti. From the qualitative analysis of the texts that describe parents’ experience, three fundamental elements emerged. The first is inherent to the mourning orientation to loss and the fear of death; the second to the disenfranchisement of mourning and transgender identity between family and society; and the third illustrates the final restorative outcome of mourning.