Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield

Intellectual disability (ID) is a measurable phenotypic consequence of genetic and environmental factors. In this study, we prospectively assessed the diagnostic yield of genomic tools (molecular karyotyping, multi-gene panel and exome sequencing) in a cohort of 337 ID subjects as a first-tier test and compared it with a standard clinical evaluation performed in parallel. Standard clinical evaluation suggested a diagnosis in 16% of cases (54/337) but only 70% of these (38/54) were subsequently confirmed. On the other hand, the genomic approach revealed a likely diagnosis in 58% (n=196). These included copy number variants in 14% (n=54, 15% are novel), and point mutations revealed by multi-gene panel and exome sequencing in the remaining 43% (1% were found to have Fragile-X). The identified point mutations were mostly recessive (n=117, 81%), consistent with the high consanguinity of the study cohort, but also X-linked (n=8, 6%) and de novo dominant (n=19, 13%). When applied directly on all cases with negative molecular karyotyping, the diagnostic yield of exome sequencing was 60% (77/129). Exome sequencing also identified likely pathogenic variants in three novel candidate genes (DENND5A, NEMF and DNHD1) each of which harbored independent homozygous mutations in patients with overlapping phenotypes. In addition, exome sequencing revealed de novo and recessive variants in 32 genes (MAMDC2, TUBAL3, CPNE6, KLHL24, USP2, PIP5K1A, UBE4A, TP53TG5, ATOH1, C16ORF90, SLC39A14, TRERF1, RGL1, CDH11, SYDE2, HIRA, FEZF2, PROCA1, PIANP, PLK2, QRFPR, AP3B2, NUDT2, UFC1, BTN3A2, TADA1, ARFGEF3, FAM160B1, ZMYM5, SLC45A1, ARHGAP33 and CAPS2), which we highlight as potential candidates on the basis of several lines of evidence, and one of these genes (SLC39A14) was biallelically inactivated in a potentially treatable form of hypermanganesemia and neurodegeneration. Finally, likely causal variants in previously published candidate genes were identified (ASTN1, HELZ, THOC6, WDR45B, ADRA2B and CLIP1), thus supporting their involvement in ID pathogenesis. Our results expand the morbid genome of ID and support the adoption of genomics as a first-tier test for individuals with ID.

Fiber gene based molecular and biological characterization of hydropericardium-hepatitis syndrome associated avian adenoviruses

This study was designed to perform biological and molecular characterization of avian adenoviruses (AAVs) recovered from suspected cases of hydropericardium-hepatitis syndrome (HHS) in commercial poultry. Initially the samples were screened by Agar Gel Precipitation Test (AGPT) for the presence of AAVs followed by its confirmation and typing through polymerase chain reaction (PCR) focusing on already reported serotypes AAV-4, AAV-8 and AAV-10 elsewhere. These PCR-positive samples were further subjected to amplification of fiber gene, followed by conducting restriction fragment length polymorphism (RFLP) using restriction enzyme Alu. The selected isolates were further propagated through cell culture and pathogenic potential of selected isolates was determined by infecting chickens. In this study, out of a total 190 samples, 57.8% of suspected cases were found positive for AAV presence through AGPT while sub-type identification using PCR revealed 46.3% for these viruses belonging to AAV-4, 41.8% to AAV-8 and 11.8% showed co-infection of AAV-4 and AAV-8. AAV-10 was not detected in any of the tested samples. On the basis of RFLP pattern, AAV-4 isolates were further divided into four sub-groups (A-D) while AAV-8 isolates had identical RFLP pattern. To further evaluate the pathogenic potential of these sub-groups of AAV-4 isolates, specific pathogen free (SPF) chicks were challenged with selected isolates belonging to each of the sub-groups, resulting in variable pattern of pathogenicity. It is concluded that any variation in the fiber gene of AAV-4 isolates may affect its pathogenicity and eventually specificity of the vaccines used against such infections. Therefore, regular monitoring of the circulating AAV serotypes may be helpful in understanding the pathogenic potential of emerging AAVs, which may lead to development of more effective response strategies accordingly.

Health Related Quality of Life in Children with Nephrotic Syndrome in Bangladesh

Outcome of children with nephrotic syndrome has continued to improve over time. However minimal data exist to describe health-related quality of life in children with nephrotic syndrome. This cross sectional study was conducted over a period of six months to assess the health related quality of life in children with nephrotic syndrome in the Department of Pediatric Nephrology, Dhaka Medical College Hospital, Bangladesh. Fifty children (age ranged 2-12 years) with nephrotic syndrome who had three or more relapses diagnosed at least one year back receiving treatment and on follow up were included in this study. Quality of Life scores were collected using Bengali translated instruments- the Pediatric Quality of Life Inventory™ (PedsQL™) version 4.0 Generic Scale and the Pediatric Quality of Life Questionnaire for Nephrotic Syndrome proxy-report from parents. Medical data and Demographic data were collected from medical records, and from parents in outpatient department or hospital ward. Interviews of eligible guardians were performed individually to collect quality of life (QoL) scores. Among 50 children, mean±SD age of the children was 7±2.92 years. Most children were male (58%). Female parents respondent during interview were 62%, most parents (48%) were very poor in socioeconomic condition. Most children had frequent relapses (60%). Median time since diagnosis was 2 years. Regarding PedsQL scores, child age with physical summary score (p value <0.001), child age with social summary score (p value 0.003), frequent relapse with kidney disease summary score (p value 0.04) and time since diagnosis (p value <0.001) were statistically significant. In conclusion physical and social summary score were worst. Frequent relapse found to be an important factor in impaired QoL. Prolonged duration of the disease activity was associated with significant impairment of QoL.