In clinical genetic testing, checking the concordance between self-reported gender and genotype-inferred gender from genomic data is a significant quality control measure because mismatched gender due to sex chromosomal abnormalities or misregistration of clinical information can significantly affect molecular diagnosis and treatment decisions. Targeted gene sequencing (TGS) is widely recommended as a first-tier diagnostic step in clinical genetic testing. However, the existing gender-inference tools are optimized for whole genome and whole exome data and are not adequate and accurate for analyzing TGS data. In this study, we validated a new gender-inference tool, seGMM, which uses unsupervised clustering (Gaussian mixture model) to determine the gender of a sample. The seGMM tool can also identify sex chromosomal abnormalities in samples by aligning the sequencing reads from the genotype data. The seGMM tool consistently demonstrated >99% gender-inference accuracy in a publicly available 1,000-gene panel dataset from the 1,000 Genomes project, an in-house 785 hearing loss gene panel dataset of 16,387 samples, and a 187 autism risk gene panel dataset from the Autism Clinical and Genetic Resources in China (ACGC) database. The performance and accuracy of seGMM was significantly higher for the targeted gene sequencing (TGS), whole exome sequencing (WES), and whole genome sequencing (WGS) datasets compared to the other existing gender-inference tools such as PLINK, seXY, and XYalign. The results of seGMM were confirmed by the short tandem repeat analysis of the sex chromosome marker gene, amelogenin. Furthermore, our data showed that seGMM accurately identified sex chromosomal abnormalities in the samples. In conclusion, the seGMM tool shows great potential in clinical genetics by determining the sex chromosomal karyotypes of samples from massively parallel sequencing data with high accuracy.

The origins of Tibeto-Burman populations on the eastern Tibetan Plateau (TP), especially within the Tibetan-Yi Corridor, remain unresolved. We sequenced whole genomes of 293 individuals from 21 Tibeto-Burman-speaking groups and genotyped 799 individuals from 60 Sino-Tibetan-speaking groups to reconstruct regional population history. Our analyses reveal fine-scale substructure and extensive admixture along the underrepresented Tibetan-Yi and Hexi corridors, driven by gene flow from Eastern Eurasian rice/millet farmers and Western Eurasian steppe pastoralists. We estimate that Tibetans diverged from their common ancestors with Han Chinese in the early Neolithic (∼9.9 kya), followed by differentiation among Tibetan-Yi Corridor populations in the middle Neolithic (∼4.6 kya). These splits coincide with distinct cultural trajectories that produced a pronounced north–south genetic structure among Tibeto-Burman groups. QpAdm modeling indicates that northern Tibeto-Burman speakers derive most of their ancestry from Neolithic millet farmers. Along the Hexi Corridor, an essential axis of Eurasian connectivity, fine-scale analyses show a dominant legacy of millet-farming populations with additional ancestry from incoming Eurasian herders. Together, these findings clarify the settlement history of eastern TP populations and underscore the role of geographic and cultural corridors in structuring ancient intercontinental gene flow across Eurasia.

Short tandem repeats (STRs) confer evolutionary advantages across various species, yet their roles in human high-altitude adaptation remain largely unexplored. In this study, we analyzed over 1.1 million STRs in 7876 whole-genome sequencing samples, including 3808 newly sequenced Tibeto-Burman (TB) speakers and Han Chinese individuals inhabiting the Qinghai-Tibet Plateau and neighboring regions. We characterized more than 570,000 polymorphic STRs across coding/noncoding genomic and functional contexts, revealing distinct STR variation patterns specific to TB speakers. Notably, divergent STRs in TB speakers were predominantly located in high-altitude adaptive genes and frequently associated with gene expression levels. Additionally, we identified over 17,000 STRs strongly associated with environmental conditions on the Qinghai-Tibet Plateau. These STRs exerted multilevel gene regulation through modulating protein coding, fine-tuning cis-regulatory elements, and modulating biological pathways. Furthermore, we observed substantial contributions of functional and adaptive STRs to human phenotypic diversity. Collectively, our findings provide genomic STR resources of TB speakers and genetic insights into their roles in human adaptive evolution.

Background: Biotinidase deficiency (OMIM 253260) is an autosomal recessively inherited disorder affecting about 1/60,000 people worldwide. The absence or deficiency of biotinidase impairs free biotin recycling and affects biotin‐dependent carboxylase functions.Methods: A Chinese patient with spontaneous recurrent epilepsy, an eczema‐like rash, hair loss, hypotonia, and hearing loss began at three months of age. Her biotinidase activity was 1.0 nmol/ml/min, 9.5% of the mean control activity, which confirmed profound biotinidase deficiency.Results: Compound heterozygous for c.250‐1G > C and c.878dupT variants in the BTD gene were identified in this patient. These two variants were novel and absent in the population matched controls and any databases.Conclusions: This study expanded the mutation spectrum of alterations of the BTD gene. Our patient also emphasized the critical role of biotinidase activity measurement combined with mutation analysis in early diagnosis of biotinidase deficiency.

Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) and primary ovarian insufficiency (POI) secondary to ovarian dysgenesis. However, the mutation spectrum of disease-causing genes for Perrault syndrome in the Chinese population remains poorly understood. In this study, we report on two Chinese families with Perrault syndrome type 3 caused by novel CLPP gene variants. We also conducted a comprehensive literature review of CLPP gene variants in Perrault syndrome type 3 to elucidate genotype-phenotype associations. Using Whole Genome Sequencing (WGS) data, two pedigrees with Perrault syndrome type 3 were ascertained in the Chinese Deafness Genetics Cohort through genotype-driven analysis. Variants were validated using Sanger sequencing and copy number quantification methods. In vitro analysis of splice site variants in the CLPP gene using the minigene assay. Two Han Chinese families were ascertained: one with compound heterozygous variants (c.270 + 1G > C and c.355A > C [p. Ile119Leu]) and the other with missense variant (c.400G > C [p. Asp134His]) together with a large deletion in CLPP. In vitro minigene assays confirmed that the c.270 + 1G > C variant causes intron 2 retention and an alternative 5’ splice site in exon 2, leading to protein alteration. Among 33 Perrault syndrome type 3 patients in literature, 97% (31/32) had hearing loss, 55% (16/29) neurological disease, and 71% (15/21) females had POI. Including our 4 novel variants, 21 pathogenic CLPP gene variants have been reported, with 57% (12/21) missense and 43% (9/21) truncating variants, mainly in the ATP-dependent Clp protease proteolytic subunit. Biallelic truncating or missense plus truncating genotypes showed higher rates of neurological disease (p = 0.001), but no significant difference in hearing loss incidence compared to biallelic missense genotypes was observed. This study highlights the challenges in diagnosing Perrault syndrome due to its genetically and clinically heterogeneity. By exploring novel variants and establishing genotype-phenotype correlations, we aim to improve the genetic diagnosis and consultation for this complex disorder.