KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variation

Functional impact and evolution of a novel human polymorphic inversion that disrupts a gene and creates a fusion transcript

Since the discovery of chromosomal inversions almost 100 years ago, how they are maintained in natural populations has been a highly debated issue. One of the hypotheses is that inversion breakpoints could affect genes and modify gene expression levels, although evidence of this came only from laboratory mutants. In humans, a few inversions have been shown to associate with expression differences, but in all cases the molecular causes have remained elusive. Here, we have carried out a complete characterization of a new human polymorphic inversion and determined that it is specific to East Asian populations. In addition, we demonstrate that it disrupts the ZNF257 gene and, through the translocation of the first exon and regulatory sequences, creates a previously nonexistent fusion transcript, which together are associated to expression changes in several other genes. Finally, we investigate the potential evolutionary and phenotypic consequences of the inversion, and suggest that it is probably deleterious. This is therefore the first example of a natural polymorphic inversion that has position effects and creates a new chimeric gene, contributing to answer an old question in evolutionary biology

Genetic analysis of haemophilia A in Bulgaria

BACKGROUND: Haemophilias are the most common hereditary severe disorders of blood clotting. In families afflicted with heamophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostical strategy for carriership determination and prenatal diagnostics of haemophilia A in Bulgarian haemophilic population. METHODS: A diagnostical strategy consisting of screening for most common mutations in the factor VIII gene and analysis of a panel of eight linked to the factor VIII gene locus polymorphisms was established. RESULTS: Polymorphic analysis for carrier status determination of haemophilia A was successful in 30 families out of 32 (94%). Carrier status was determined in 25 of a total of 28 women at risk (89%). Fourteen prenatal diagnoses in women at high risk of having a haemophilia A – affected child were performed, resulting in 6 healthy boys and 5 girls. CONCLUSION: The compound approach proves to be a highly informative and cost-effective strategy for prevention of recurrence of haemophilia A in Bulgaria. DNA analysis facilitates carriership determination and subsequent prenatal diagnosis in the majority of Bulgarian families affected by haemophilia A

Eighteen Years of Molecular Genotyping the Hemophilia Inversion Hotspot: From Southern Blot to Inverse Shifting-PCR

The factor VIII gene (F8) intron 22 inversion (Inv22) is a paradigmatic duplicon-mediated rearrangement, found in about one half of patients with severe hemophilia A worldwide. The identification of this prevalent cause of hemophilia was delayed for nine years after the F8 characterization in 1984. The aim of this review is to present the wide diversity of practical approaches that have been developed for genotyping the Inv22 (and related int22h rearrangements) since discovery in 1993. The sequence— Southern blot, long distance-PCR and inverse shifting-PCR—for Inv22 genotyping is an interesting example of scientific ingenuity and evolution in order to resolve challenging molecular diagnostic problems

Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM

<p>Abstract</p> <p>Background</p> <p>Hemophilia A represents the most common and severe inherited hemorrhagic disorder. It is caused by mutations in the F8 gene, which leads to a deficiency or dysfunctional factor VIII protein, an essential cofactor in the factor X activation complex.</p> <p>Methods</p> <p>We used long-distance polymerase chain reaction and denaturing high performance liquid chromatography for mutation scanning of the F8 gene. We designed the competitive multiplex PCR to identify the carrier with exonal deletions. In order to facilitate throughput and minimize the cost of mutation scanning, we also evaluated a new mutation scanning technique, high resolution melting analysis (HRM), as an alternative screening method.</p> <p>Results</p> <p>We presented the results of detailed screening of 122 Taiwanese families with hemophilia A and reported twenty-nine novel mutations. There was one family identified with whole exons deletion, and the carriers were successfully recognized by multiplex PCR. By HRM, the different melting curve patterns were easily identified in 25 out of 28 cases (89%) and 15 out of 15 (100%) carriers. The sensitivity was 93 % (40/43). The overall mutation detection rate of hemophilia A was 100% in this study.</p> <p>Conclusion</p> <p>We proposed a diagnostic strategy for hemophilia A genetic diagnosis. We consider HRM as a powerful screening tool that would provide us with a more cost-effective protocol for hemophilia A mutation identification.</p

Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A

Mutations in the factor VIII gene have been discovered for barely more than half of the examined cases of severe haemophilia A. To account for the unidentified mutations, we propose a model based on the possibility of recombination between homologous sequences located in intron 22 and upstream of the factor VIII gene. Such a recombination would lead to an inversion of all intervening DNA and a disruption of the gene. We present evidence to support this model and describe a Southern blot assay that detects the inversion. These findings should be valuable for genetic prediction of haemophilia A in approximately 45% of families with severe disease

Common Buckthorn Engineered Biochar (Rhamnus Cathartica), Calcined Quagga Mussel Shells (Dreissena Rostriformis), Pickled Steel, and Steel Slag as Filter Media for the Sorption of Phosphorus from Agricultural Runoff

The reuse of waste residuals as reactive media is a sustainable solution to remove phosphorus (P) from wastewater and reduce eutrophication. Large reactive waste media filters incorporated in edge-of-field treatment systems could reduce P loading from agricultural fields. We measured the treatment potential of regionally available waste residuals (i.e., calcined quagga mussel shells (CSHELL), magnesium activated biochar (MGBC), pickled steel (PSTEEL), and steel slag (SLAG)) for dissolved P removal. CSHELL and MGBC had elevated sorption capacities (64,419 and 50,642 mg kg−1, respectively) in comparison to SLAG and PSTEEL (14,541 mg kg−1 and 736 mg kg−1, respectively). However, CSHELL requires long reaction times for removal (22% removal after 1.5 h) and P sorbed to MGBC is removed with DI, reducing treatment potential. SLAG and PSTEEL were the only media with significant reductions of agricultural runoff and had the greatest overall treatment potential. SLAG is recommended for removal and replacement systems while PSTEEL is suitable for larger systems designed for regeneration on site

Common Buckthorn Engineered Biochar (Rhamnus Cathartica), Calcined Quagga Mussel Shells (Dreissena Rostriformis), Pickled Steel, and Steel Slag as Filter Media for the Sorption of Phosphorus from Agricultural Runoff

The reuse of waste residuals as reactive media is a sustainable solution to remove phosphorus (P) from wastewater and reduce eutrophication. Large reactive waste media filters incorporated in edge-of-field treatment systems could reduce P loading from agricultural fields. We measured the treatment potential of regionally available waste residuals (i.e., calcined quagga mussel shells (CSHELL), magnesium activated biochar (MGBC), pickled steel (PSTEEL), and steel slag (SLAG)) for dissolved P removal. CSHELL and MGBC had elevated sorption capacities (64,419 and 50,642 mg kg&minus;1, respectively) in comparison to SLAG and PSTEEL (14,541 mg kg&minus;1 and 736 mg kg&minus;1, respectively). However, CSHELL requires long reaction times for removal (22% removal after 1.5 h) and P sorbed to MGBC is removed with DI, reducing treatment potential. SLAG and PSTEEL were the only media with significant reductions of agricultural runoff and had the greatest overall treatment potential. SLAG is recommended for removal and replacement systems while PSTEEL is suitable for larger systems designed for regeneration on site