Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases.

BACKGROUND: Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS: In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS: Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS: Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.

Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families.

Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.

Malaria helminth co-infections and their contribution for aneamia in febrile patients attending Azzezo health center, Gondar, Northwest Ethiopia: a cross sectional study.

OBJECTIVE: To assess the prevalence of malaria helminth co-infections and their contribution for aneamia in febrile patients attending Azzezo health center, Gondar, Northwest Ethiopia. METHODS: A cross section study was conducted among febrile patients attending Azezo health center from February-March 30, 2011. Convenient sampling technique was used to select 384 individuals. Both capillary blood and stool were collected. Giemsa stained thick and thin blood film were prepared for identification of Plasmodium species and stool sample was examined by direct wet mount and formalin-ether concentration technique for detection of intestinal helminthes parasites. Haemoglobin concentration was determined using a portable haemoglobin spectrophotometer, Hemocue Hb 201 analyzer. RESULTS: Out of 384 febrile patients examined for malaria parasites, 44 (11.5%) individuals were positive for malaria parasites, of which Plasmodium vivax accounted for 75.0% (33), Plasmodium falciparum for 20.5% (9) infectious, whereas two person (4.5%) had mixed species infection. Prevalence of malaria was higher in males (28) when compared with prevalence in females (16). More than half (207, 53.9%) of study participants had one or more infection. Prevalence was slightly higher in females (109, 52.7%) than in males (98, 47.3%). About helminths, Ascaris lumbricoides was the predominant isolate (62.1%) followed by hookworms (18.4%). Only 22 participants were co-infected with malaria parasite and helminths and co-infection with Ascaris lumbricoides was predominant (45.0%). The prevalence of anemia was 10.9% and co-infection with Plasmodium and helminth parasites was significantly associated with (P< 0.000 1) higher anemia prevalence compared to individuals without any infection. CONCLUSIONS: Prevalence of malaria and soil transmitted helminths is high and the disease is still major health problem in the study area. Hence, simultaneous combat against the two parasitic infections is very crucial to improve health of the affected communities in economically developing countries.