No abstract

Breast cancer is the most commonly diagnosed cancer in women, with 10% of disease attributed to hereditary factors. Although BRCA1 and BRCA2 account for a high percentage of hereditary cases, there are more than 25 susceptibility genes that differentially impact the risk for breast cancer. Traditionally, germline testing for breast cancer was performed by Sanger dideoxy terminator sequencing in a reflexive manner, beginning with BRCA1 and BRCA2. The introduction of next-generation sequencing (NGS) has enabled the simultaneous testing of all genes implicated in breast cancer resulting in diagnostic labs offering large, comprehensive gene panels. However, some physicians prefer to only test for those genes in which established surveillance and treatment protocol exists. The NGS based BRCAplus test utilizes a custom tiled PCR based target enrichment design and bioinformatics pipeline coupled with array comparative genomic hybridization (aCGH) to identify mutations in the six high-risk genes: BRCA1, BRCA2, PTEN, TP53, CDH1, and STK11. Validation of the assay with 250 previously characterized samples resulted in 100% detection of 3,025 known variants and analytical specificity of 99.99%. Analysis of the clinical performance of the first 3,000 BRCAplus samples referred for testing revealed an average coverage greater than 9,000X per target base pair resulting in excellent specificity and the sensitivity to detect low level mosaicism and allele-drop out. The unique design of the assay enabled the detection of pathogenic mutations missed by previous testing. With the abundance of NGS diagnostic tests being released, it is essential that clinicians understand the advantages and limitations of different test designs.

Elongator is a multi-subunit protein complex essential to transcription elongation, histone acetylation, and tRNA modification. The complex consists of six highly conserved protein subunits, called Elongator Proteins (ELP) 1-6. Apart from an association with intellectual disability (ID), there is limited clinical information about patients with ELP2 variants. Here we report on two brothers with severe ID, spastic diplegia, and self-injury whose presentation eluded a diagnosis for over 20 years. In both brothers, whole exome sequencing revealed a likely pathogenic, compound heterozygous missense variant in ELP2. We describe the phenotype and natural history of the ELP2-related disorder in these brothers.

Objective: We describe a novel congenital motor neuron disease with early demise due to respiratory insufficiency with clinical overlap with spinal muscular atrophy with respiratory distress (SMARD) type 1 but lacking a mutation in the IGHMBP2 gene.Methods: Exome sequencing was used to identify a de novo mutation in the LAS1L gene in the proband. Pathogenicity of the mutation was validated using a zebrafish model by morpholinomediated knockdown of las1l.Results: We identified a de novo mutation in the X-linked LAS1L gene in the proband (p.S477N).The mutation is in a highly conserved region of the LAS1L gene predicted to be deleterious by bioinformatic analysis. Morpholino-based knockdown of las1l, the orthologous gene in zebrafish, results in early lethality and disruption of muscle and peripheral nerve architecture. Coinjection of wild-type but not mutant human RNA results in partial rescue of the phenotype. Conclusion:We report a patient with a SMARD phenotype due to a mutation in LAS1L, a gene important in coordinating processing of the 45S pre-rRNA and maturation of the large 60S ribosomal subunit. Similarly, the IGHMB2 gene associated with SMARD type 1 has been suggested to have an important role in ribosomal biogenesis from its role in processing the 45S pre-rRNA. We propose that disruption of ribosomal maturation may be a common pathogenic mechanism linking SMARD phenotypes caused by both IGHMBP2 and LAS1L. Spinal muscular atrophy with respiratory distress (SMARD) is a rare autosomal recessive disorder of neonatal weakness and early respiratory failure (Online Mendelian Inheritance in Man [OMIM] #604320). 1 SMARD was first described in 1974 as a variant of WerdnigHoffmann disease (spinal muscular atrophy type I) but is distinguished by the prominence of early respiratory failure and distal muscle weakness or joint contractures.2 Since discovery of the IGHMBP2 gene as a cause for SMARD, 3 appreciation of the clinical and genetic heterogeneity has been increasing.2,4,5 IGHMBP2 is a ubiquitously expressed helicase that colocalizes with factors controlling RNA splicing in the cytosol and nucleus. 6 A role for IGHMBP2 in translation has been proposed based on colocalization in the cytoplasm with ribosomal proteins and ribosomal RNA (rRNA). 6,7 As in many other disorders with motor neuron involvement, it is unclear why mutations in IGHMBP2 have a disproportionate effect on motor neurons. 8Infants presenting with a SMARD phenotype but lacking mutations in IGHMBP2 are common, accounting for up to two-thirds of reported patients. 4,9 We describe an infant who presented with distal weakness and primary respiratory failure associated with diaphragm paralysis but lacking a