Molecular characterization of the Yp11.2 region deletion in the Chinese Han population

Pang, Qianqian; Lin, Qingai; Wang, Di; Sun, Zheng; Wang, Junfang

doi:10.1007/s00414-021-02596-x

Cited by 3 publications

(3 citation statements)

References 25 publications

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“…Altogether, we can only hypothesise that the false identification of sample 14 is due to either a miss labelling of the tooth or to the absence of AMELY from the sample itself, which could be caused by a deletion of the AMELY gene on the Y chromosome [43][44][45][46] .…”

Section: Use Of a Validation Cohort For Assessing The Performance Of ...mentioning

confidence: 99%

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Koenig,

Bortel,

Paterson

et al. 2024

Preprint

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Biological sex is key information for archaeological and forensic studies, which can be determined by proteomics. However, lack of a standardised approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to high-resolution parallel reaction monitoring assay allowing for a throughput of 200 samples-per-day with high quantitative performance enabling confident identification of both males and females. Additionally, we have developed a streamlined data analysis pipeline and integrated it into an R-Shiny interface for ease-of-use. The method was first developed and optimised using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archaeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by tenfold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archaeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens.

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Section: Use Of a Validation Cohort For Assessing The Performance Of ...mentioning

confidence: 99%

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Koenig,

Bortel,

Paterson

et al. 2024

Preprint

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“…Because of the large length of the deletion region, NGS technology with a shorter read length is useless in this type of sequence detection. Most of the deletion or duplication of CNV in this region is only in Yp11.2, which does not contain the TSPY multicopy region and other ampliconic regions; therefore, it does not show reproductive disorders ( Pang et al, 2021a ). Except for the TSPY array, it seems that the direct relationship between CNV in the Yp region and spermatogenesis is not that obvious ( Murphy et al, 2007 ; Nardello et al, 2021 ).…”

Section: Repetitive Sequences Of the Y Chromosomementioning

confidence: 99%

“…Reports have indicated that the gene is only transcribed in the testis and expresses a protein of 108 amino acids (Skaletsky et al, 2003;Jangravi et al, 2013;Alechine and Corach, 2014), although the two copies may have different roles in spermatogenesis (Noordam et al, 2011;Lu et al, 2014). GOLGA2 is a Golgi matrix protein that is essential for the processing and transport of specific proteins by the Golgi (Liu C. et al, 2017;Pang et al, 2021b). Moreover, the deletion of GOLGA2 can cause male sterility by regulating the function of the acrosome (Han et al, 2017).…”

Section: Structurementioning

confidence: 99%

Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility

Xu¹,

Pang

2022

Front. Cell Dev. Biol.

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The male-specific Y chromosome, which is well known for its diverse and complex repetitive sequences, has different sizes, genome structures, contents and evolutionary trajectories from other chromosomes and is of great significance for testis development and function. The large number of repetitive sequences and palindrome structure of the Y chromosome play an important role in maintaining the stability of male sex determining genes, although they can also cause non-allelic homologous recombination within the chromosome. Deletion of certain Y chromosome sequences will lead to spermatogenesis disorders and male infertility. And Y chromosome genes are also involved in the occurrence of reproductive system cancers and can increase the susceptibility of other tumors. In addition, the Y chromosome has very special value in the personal identification and parentage testing of male-related cases in forensic medicine because of its unique paternal genetic characteristics. In view of the extremely high frequency and complexity of gene rearrangements and the limitations of sequencing technology, the analysis of Y chromosome sequences and the study of Y-gene function still have many unsolved problems. This article will introduce the structure and repetitive sequence of the Y chromosome, summarize the correlation between Y chromosome various sequence deletions and male infertility for understanding the repetitive sequence of Y chromosome more systematically, in order to provide research motivation for further explore of the molecules mechanism of Y-deletion and male infertility and theoretical foundations for the transformation of basic research into applications in clinical medicine and forensic medicine.

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Enamel proteins reveal biological sex and genetic variability within southern AfricanParanthropus

Madupe,

Koenig,

Patramanis

et al. 2023

Preprint

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The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. ForParanthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa1,2and the nature of intraspecific variation3-6are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically toP. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern AfricanParanthropus, as previously suggested based on morphology alone6. Finally, the molecular data also confirm the taxonomic placement ofParanthropuswithin the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

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Molecular characterization of the Yp11.2 region deletion in the Chinese Han population

Cited by 3 publications

References 25 publications

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Automated high-throughput biological sex identification from archaeological human dental enamel using targeted proteomics

Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility

Enamel proteins reveal biological sex and genetic variability within southern AfricanParanthropus

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