Abstract P42: Genetic Variants Associated With Vasospasm Following Aneurysmal Subarachnoid Hemorrhage

Background: Cerebral vasospasm is a major contributor to poor clinical outcomes in intracranial aneurysm (IA) patients and is involved in delayed cerebral ischemia (DCI) after aneurysmal subarachnoid hemorrhage (aSAH). Little is known about the genetic factors associated with vasospasm pathogenesis. We performed a genome-wide association study (GWAS) to investigate association of common genetic variants with risk of vasospasm in IA patients with SAH. Methods: Our Caucasian cohort of 190 aSAH patients (121 with vasospasm diagnosed by angiography) were genotyped using UK Biobank Axiom Arrays. Genotypes were called using the Best Practices Workflow in the Axiom Analysis Suite v4.0.3.3. All samples had >97% call rate, one sample was removed due to sex mismatch, and a total of 634,781 single nucleotide polymorphisms (SNPs) with >0.01 minor allele frequency were analyzed for association with vasospasm in the final cohort of 189 cases (66.7% female, mean age 54.8 years). Logistic regression analysis was performed using an additive model adjusting for age at onset of symptoms and sex. Genome-wide significance was based on Bonferroni correction for multiple testing (P< 7.9x10 -8 ). Results: No SNPs were significantly associated with vasospasm at the genome-wide level. However, eleven SNPs were nominally associated with vasospasm (P<10E-5) including the most significant SNP mapping to an intron of GLIS3 (P=9.74E-06, OR=3.94, 95% CI: 2.15-7.22), three intronic SNPs mapping to ACVR1 , and additional SNPs mapping to introns in FSTL3 , TMEM242 , DCLK1 , one SNP upstream of RAC2 and two SNPs downstream of TEX29 and TGFBR3 , and one missense SNP mapping to MYO18B. Interestingly, two of these genes ( ACVR1 and TGFBR3 ) are in the transforming growth factor-beta (TGF-beta) signaling pathway, previously implicated in SAH pathogenesis. Conclusions: We performed a GWAS of vasospasm following aSAH. Our study suggests that common SNPs may contribute to vasospasm susceptibility following aSAH and suggests a potential role for TGF-beta signaling pathway genes in vasospasm. These findings warrant further replication in additional independent studies including other DCI outcomes.

Homozygous variants in the HEXB and MBOAT7 genes underlie neurological diseases in consanguineous families

Background Neurological disorders are a common cause of morbidity and mortality within Pakistani populations. It is one of the most important challenges in healthcare, with significant life-long socio-economic burden. Methods We investigated the cause of disease in three Pakistani families in individuals with unexplained autosomal recessive neurological conditions, using both genome-wide SNP mapping and whole exome sequencing (WES) of affected individuals. Results We identified a homozygous splice site variant (NM_000521:c.445 + 1G > T) in the hexosaminidase B (HEXB) gene confirming a diagnosis of Sandhoff disease (SD; type II GM2-gangliosidosis), an autosomal recessive lysosomal storage disorder caused by deficiency of hexosaminidases in a single family. In two further unrelated families, we identified a homozygous frameshift variant (NM_024298.3:c.758_778del; p.Glu253_Ala259del) in membrane-bound O-acyltransferase family member 7 (MBOAT7) as the likely cause of disease. MBOAT7 gene variants have recently been identified as a cause of intellectual disability (ID), seizures and autistic features. Conclusions We identified two metabolic disorders of lipid biosynthesis within three Pakistani families presenting with undiagnosed neurodevelopmental conditions. These findings enabled an accurate neurological disease diagnosis to be provided for these families, facilitating disease management and genetic counselling within this population. This study consolidates variation within MBOAT7 as a cause of neurodevelopmental disorder, broadens knowledge of the clinical outcomes associated with MBOAT7-related disorder, and confirms the likely presence of a regionally prevalent founder variant (c.758_778del; p.Glu253_Ala259del) in Pakistan.

MNS1 variant associated with situs inversus and male infertility

Ciliopathy disorders due to abnormalities of motile cilia encompass a range of autosomal recessive conditions typified by chronic otosinopulmonary disease, infertility, situs abnormalities and hydrocephalus. Using a combination of genome-wide SNP mapping and whole exome sequencing (WES), we investigated the genetic cause of a form of situs inversus (SI) and male infertility present in multiple individuals in an extended Amish family, assuming that an autosomal recessive founder variant was responsible. This identified a single shared (2.34 Mb) region of autozygosity on chromosome 15q21.3 as the likely disease locus, in which we identified a single candidate biallelic frameshift variant in MNS1 [NM_018365.2: c.407_410del; p.(Glu136Glyfs*16)]. Genotyping of multiple family members identified randomisation of the laterality defects in other homozygous individuals, with all wild type or MNS1 c.407_410del heterozygous carriers being unaffected, consistent with an autosomal recessive mode of inheritance. This study identifies an MNS1 variant as a cause of laterality defects and male infertility in humans, mirroring findings in Mns1-deficient mice which also display male infertility and randomisation of left–right asymmetry of internal organs, confirming a crucial role for MNS1 in nodal cilia and sperm flagella formation and function.

Location deviations of DNA functional elements affected SNP mapping in the published databases and references

The recent extensive application of next-generation sequencing has led to the rapid accumulation of multiple types of data for functional DNA elements. With the advent of precision medicine, the fine-mapping of risk loci based on these elements has become of paramount importance. In this study, we obtained the human reference genome (GRCh38) and the main DNA sequence elements, including protein-coding genes, miRNAs, lncRNAs and single nucleotide polymorphism flanking sequences, from different repositories. We then realigned these elements to identify their exact locations on the genome. Overall, 5%–20% of all sequence element locations deviated among databases, on the scale of kilobase-pair to megabase-pair. These deviations even affected the selection of genome-wide association study risk-associated genes. Our results implied that the location information for functional DNA elements may deviate among public databases. Researchers should take care when using cross-database sources and should perform pilot sequence alignments before element location-based studies.

High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat

The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex, consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, and 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074, and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. The SSR- and DArT-based genetic maps had an average distance of 6.5, 7.8, and 9.7 cM between marker loci for populations EGA/Millewa, P92201D5/P91193D1, and 6HRWSN125/WAWHT2074, respectively. This study used single nucleotide polymorphism (SNP) markers from the iSelect Infinium 90K genotyping array to fine-map genomic regions harbouring QTL for flag leaf and glume SNB resistance, reducing the average distance between markers to 2.9, 3.3, and 3.4 cM for populations P92201D5/P91193D1, EGA/Millewa, and 6HRWSN125/WAWHT2074, respectively. Increasing the marker density of the genetic maps with SNPs did not identify any new QTL for SNB resistance but discriminated previously identified co-located QTL into separate but closely linked QTL.