SNP Array Screening and Long Range PCR-Based Targeted Next Generation Sequencing for Autosomal Recessive Disease with Consanguinity: Insight from a Case of Xeroderma Pigmentosum Group C.

Advances in genetic technologies have made genetic testing more accessible than ever before. However, depending on national, regional, legal, and health insurance circumstances, testing procedures may still need to be streamlined in real-world clinical practice. In cases of autosomal recessive disease with consanguinity, the mutation locus is necessarily isodisomy because both alleles originate from a common ancestral chromosome. Based on this premise, we implemented integrated genetic diagnostic methods using SNP array screening and long range PCR-based targeted NGS in a Japanese patient with xeroderma pigmentosum (XP) under the limitation of the national health insurance system. SNP array results showed isodisomy only in XPC and ERCC4 loci. NGS, with a minimal set of long-range PCR primers, detected a homozygous frameshift mutation in XPC; NM_004628.5:c.218_219insT p.(Lys73AsnfsTer9), confirmed by Sanger sequencing, leading to a rapid diagnosis of XP group C. This shortcut strategy is applicable to all autosomal recessive diseases caused by consanguineous marriages, especially in scenarios with a moderate number of genes to test, a common occurrence in clinical genetic practice.

The chicken-derived velogenic Newcastle disease virus can acquire high pathogenicity in domestic ducks via serial passaging.

Velogenic Newcastle disease virus (NDV) strains, which show high mortality in chickens, generally do not cause severe disease in waterfowl such as ducks. To elucidate the difference in the pathogenic mechanisms of NDV between chickens and ducks, a chicken-derived velogenic strain (9a5b) was passaged in domestic ducks five times in their air sacs, followed by 20 times in their brains. Eventually, 9a5b acquired higher intracerebral and intranasal pathogenicity in ducks. The intracerebral pathogenicity index (ICPI) value increased from 1.10 to 1.88. All one-week-old ducks intranasally inoculated with the passaged virus (d5a20b) died by 5 days post-inoculation, whereas 70% of the ducks inoculated with parental 9a5b survived for 8 days. The d5a20b strain replicated in broader systemic tissues in ducks compared with the 9a5b strain. The velogenic profile of 9a5b in chickens was maintained after passaging in ducks. The d5a20b suppressed IFN-ß gene expression in duck embryo fibroblasts and replicated more rapidly than 9a5b. A total of 11 amino acid substitutions were found in the P, V, M, F, HN, and L proteins of d5a20b. These results suggest that chicken-derived velogenic NDVs have the potential to become virulent in both chickens and ducks during circulation in domesticated waterfowl populations. RESEARCH HIGHLIGHTSChicken-derived NDV acquired high pathogenicity in ducks with serial passaging.The passaged NDV showed intracerebral and intranasal pathogenicity in ducks.The passaged NDV efficiently replicated in systemic tissues in ducks.Of 11 amino acid substitutions some or all are likely involved in pathogenicity.

Scalp microbiota in members of a Japanese high school judo team including Trichophyton tonsurans carriers.

Trichophyton tonsurans is a major causative fungus of human dermatophytosis, which has been isolated from contact sport players in Japan. The microbiome in the scalp of judoists with or without T. tonsurans infection was analyzed to investigate the correlation between T. tonsurans infection and microbiome profile. Among 30 members of the same judo team in a high school, samples were collected by scrubbing their scalp with shampoo hairbrushes; then, DNA was extracted directly from the obtained scales. Twenty-seven datasets were subjects for microbiome analysis and T. tonsurans was detected in six members (no T. tonsurans-positive participants had scalp lesions). Regarding the fungal microbiome, Cyphellophora were more abundant in the T. tonsurans-positive group (TP) than T. tonsurans-negative group (TN) (P < 0.05). Regarding the Malassezia microbiome, Malassezia caprae were more abundant in TP than TN (P < 0.01). Regarding the bacterial microbiome, Lactococcus, Actinobacillus, Beijerinckiaceae and Xanthomonas were more abundant in TP than TN (P < 0.05). Also, the Shannon diversity index revealed no significant diversity between TP and TN, and 3-D principal coordinate analysis revealed no clear separation between TP and TN. There was practically no difference in microbiome between TP and TN, indicating that T. tonsurans could colonize humans regardless of their original microbiome. T. tonsurans coexisted with other fungi and bacteria without affecting species diversity in asymptomatic carriers. To our knowledge, this is the first investigation of the correlation between T. tonsurans infection and microbiome profile.