Human Genome Variation最新文献

Here we present the construction of JG2, an updated population-specific reference genome for the Japanese population. Utilizing data from three individuals previously used in the construction of JG1, several methodologies were employed to enhance genomic coverage and assembly quality. Hi-C sequencing technology facilitated phase-aware assembly, generating two haploid assemblies per individual and enabling improved representation of genetic variation. A meta-assembly strategy and a majority decision approach further refined assembly quality by combining the best sequences from multiple assemblies and minimizing the inclusion of rare variants. The resulting JG2 genome comprises chromosome-level sequences, mitochondrial chromosomes and unplaced scaffolds, offering more comprehensive coverage of the Japanese genome. Comparative analyses with other reference genomes demonstrated the accuracy and representativeness of JG2, highlighting its utility for genetic research involving the Japanese population. Overall, by adopting the phased assembly technique, JG2 represents a substantial advancement over the collapsed assembly-based JG1, with improvements including a greater number of identified variants (3,115,695 variants, of which 298,644 had an allele frequency (AF) of 1.0 in the 3.5KJPNv2 AF panel) and a higher N50 value (152,668,378 bp). These enhancements provide researchers with a more precise and comprehensive resource for understanding the genetic landscape of the Japanese population. The sequences and annotations are available on the jMorp website ( https://jmorp.megabank.tohoku.ac.jp/ ).

Here we report a Japanese patient with juvenile/adult-type galactosialidosis carrying a homozygous c.692+3A>G CTSA variant. Comprehensive genetic analyses including exome sequencing, chromosomal microarray and homozygosity mapping supported biallelic inheritance of this variant and suggested a founder effect in the Japanese population. Clinically, the patient exhibited typical features of the juvenile/adult-type galactosialidosis, with growth impairment noted during adolescence as a less conspicuous but relevant observation.

Src Homology 3 Domain-containing Adaptor Protein 3 (SASH3) deficiency is an X-linked immune disorder. Here we identified a male case with a pathogenic SASH3 variant (c.1039C>T [p.Arg347Cys]) who presented with osteogenesis imperfecta, intellectual disability and recurrent infections. While immunological features in this case were characterized, further studies are needed to determine the association between the SASH3 variant and the skeletal or neurological manifestations.

Here, using whole-exome sequencing of a cohort of 17 Japanese patients with 46,XY disorders or differences of sex development, we identified two pathogenic DEAH-box helicase 37 (DHX37) variants in three patients. We also identified a patient with a likely pathogenic variant in SOX9 and a rare likely benign variant in DHX37. This Data Report highlights the genetic and phenotypic diversity of DXH37 variants.

Here we present a case of Dravet syndrome in which a novel heterozygous deletion involving the promoter region of the SCN1A gene was identified using next-generation sequencing and multiple ligation-dependent probe amplification. This microdeletion is believed to reduce SCN1A transcription, leading to haploinsufficiency. This case highlights the importance of early genetic analysis, including that of promoter regions, before the diagnostic criteria are met for the induction of specific treatments.

Here we report a heterozygous missense variant in the ACTB gene, NM_001101.5:c.209C>T (p.Pro70Leu), detected in a case of a mildly affected infant with Baraitser-Winter cerebrofrontofacial syndrome, characterized by unique craniofacial features, coloboma and mild developmental delay, but without lissencephaly. Baraitser-Winter cerebrofrontofacial syndrome cases with a similar mild phenotype have been reported to have the same variant in different populations, suggesting a genotype-phenotype correlation in this syndrome.

Little information is available about CCR5-Δ32 and HLA-B*57:01 alleles in the Peruvian population, especially in human immunodeficiency virus (HIV)-negative people with high-risk sexual behavior. Here we describe the prevalence of these alleles in HIV-exposed seronegative individuals (PS) and HIV-seropositive individuals (PVV). For this purpose, 300 individuals were recruited: 150 from each group, and the selected alleles were characterized by endpoint PCR, real-time PCR and DNA sequencing. According to our results, the prevalence of CCR5/CCR5-Δ32 heterozygous was 2.7%, and no homozygous cases were found. The population was in Hardy-Weinberg equilibrium for the CCR5 locus. Regarding HLA-B*57:01, one case was identified in the PS group, while no cases were observed in the PVV group. No statistical difference was detected between groups (P > 0.05). In conclusion, we showed a low prevalence for CCR5-Δ32 as HLA-B*57:01 in the Peruvian population. As these alleles were found at similar frequencies among both HIV-positive and HIV-negative Peruvian individuals with high-risk sexual behavior, it is possible that other genetic factors play an important role in preventing HIV transmission in this population. The low frequency of the HLA-B*57:01 allele in the Peruvian population suggests that routine genotyping tests for abacavir hypersensitivity should be reevaluated in the public health policies of Peru's Ministry of Health, based on national epidemiological data.

Tricho-hepato-enteric syndrome (THES), a rare autosomal recessive disorder caused by variants in the SKIC3 or SKIC2 gene, is characterized by intractable diarrhea, woolly hair, growth restriction and liver disease. Here we report a neonatal case of THES with neonatal hemochromatosis, in which the novel compound heterozygous SKIC3 variants NM_014639.4:c.815_816del p.(Gly272AlafsTer9) and NM_014639.4:c.2284G>A p.(Gly762Arg) were identified. Further research is needed to elucidate the mechanisms underlying iron metabolism dysregulation in THES.

Hereditary cerebral small vessel diseases (CSVDs) include cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) caused by NOTCH3, cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy caused by biallelic HTRA1, and heterozygous HTRA1-related CSVD. Here we report a case of a 53-year-old Japanese woman with coexisting NOTCH3 p.R75P and HTRA1 p.R166L mutations, each in the heterozygote. She presented with early-onset spastic paraparesis, frequent urination, cognitive impairment and baldness. We compared the clinical features of this case with known phenotypes of CADASIL caused by p.R75P, HTRA1-related CSVD. We reported cases with heterozygous HTRA1 p.R166L to discuss the potential synergistic effects of the coexisting variants.

Noonan syndrome (NS) is a RASopathy, a disorder caused by genetic alterations involving the Ras/mitogen-activated protein kinase pathway. It causes characteristic clinical manifestations, including facial dysmorphism and congenital cardiac defects. Occasionally, lymphoedema and recurrent cellulitis occur in patients with NS, potentially escalating to lethal conditions. Despite the frequent association of cellulitis with lymphoedema in NS, features susceptible to these complications have not been fully characterized. We encountered two patients with NS carrying RIT1 pathogenic variants, who were treated for recurrent lower leg cellulitis since their teenage years, which occasionally progressed to sepsis. Here we retrospectively examined these patients with NS and recurrent cellulitis on the background of lymphoedema and reviewed published cases of NS with lymphoedema and cellulitis up to March 2024 to elucidate the clinical and genetic features of this subgroup. Our literature review identified 16 additional patients with NS with similar complications. Among the 18 patients (15 men), genetic analyses revealed pathogenic variants in PTPN11 and RIT1 in 4 patients each, with the latter occurring more frequently than commonly observed. The patients developed lymphoedema by 15 years of age, predisposing them to cellulitis by 23 years of age. Notably, four of the five patients with sepsis had congenital heart defects, with a higher prevalence than that generally reported in NS. This study highlights the characteristics of genetic variants, congenital cardiac anomalies and heightened risk of recurrent cellulitis in patients with NS, emphasizing the need for early intervention with prophylactic antibiotics and surgical treatment to mitigate these risks.