Clinical genome sequencing: Three years' experience at a tertiary children's hospital.

PURPOSE: Genome sequencing (GS) may shorten the diagnostic odyssey for patients, but clinical experience with this assay in nonresearch settings remains limited. Texas Children's Hospital began offering GS as a clinical test to admitted patients in 2020, providing an opportunity to study GS utilization, possibilities for test optimization, and testing outcomes. METHODS: We retrospectively reviewed GS orders for admitted patients for a nearly 3-year period from March 2020 through December 2022. We gathered anonymized clinical data from the electronic health record to answer the study questions. RESULTS: The diagnostic yield over 97 admitted patients was 35%. The majority of GS clinical indications were neurologic or metabolic (61%) and most patients were in intensive care (58%). Tests were often characterized as candidates for intervention/improvement (56%), frequently because of redundancy with prior testing. Patients receiving GS without prior exome sequencing (ES) had higher diagnostic rates (45%) than the cohort as a whole. In 2 cases, GS revealed a molecular diagnosis that is unlikely to be detected by ES. CONCLUSION: The performance of GS in clinical settings likely justifies its use as a first-line diagnostic test, but the incremental benefit for patients with prior ES may be limited.

The germline p53 activation syndrome: A new patient further refines the clinical phenotype.

The tumor suppressor p53 has well known roles in cancer development and germline cancer predisposition disorders, but increasing evidence supports the role of activation of this transcription factor in the pathogenesis of inherited bone marrow failure and chromosomal instability disorders. Here we report a patient with red cell aplasia, which was steroid responsive, as well as intellectual disability, seizures, microcephaly, short stature, cellular radiosensitivity, and normal telomere lengths, who had a germline heterozygous C-terminal frameshift variant in TP53 similar to others that activate the transcription factor. This is the third reported individual with a germline p53 activation syndrome, with several unique features that refine the clinical disease associated with these variants.

Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis.

Stroke causes significant disability and is a common cause of death worldwide. Previous studies have estimated that 1%-5% of stroke is attributable to monogenic etiologies. We set out to assess the utility of clinical exome sequencing (ES) in the evaluation of stroke. We retrospectively analyzed 124 individuals who received ES at the Baylor Genetics reference lab between 2012 and 2021 who had stroke as a major part of their reported phenotype. Ages ranged from 10 days to 69 years. 8.9% of the cohort received a diagnosis, including 25% of infants less than 1 year old; an additional 10.5% of the cohort received a probable diagnosis. We identified several syndromes that predispose to stroke such as COL4A1-related brain small vessel disease, homocystinuria caused by CBS mutation, POLG-related disorders, TTC19-linked mitochondrial disease, and RNASEH2A associated Aicardi-Goutieres syndrome. We also observed pathogenic variants in NSD1, PKHD1, HRAS, and ATP13A2, which are genes rarely associated with stroke. Although stroke is a complex phenotype with varying pathologies and risk factors, these results show that use of exome sequencing can be highly relevant in stroke, especially for those presenting <1 year of age.

DGIdb: mining the druggable genome.

The Drug-Gene Interaction database (DGIdb) mines existing resources that generate hypotheses about how mutated genes might be targeted therapeutically or prioritized for drug development. It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially 'druggable' genes. DGIdb can be accessed at http://dgidb.org/.

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data.

MOTIVATION: Several tools exist to identify cancer driver genes based on somatic mutation data. However, these tools do not account for subclasses of cancer genes: oncogenes, which undergo gain-of-function events, and tumor suppressor genes (TSGs) which undergo loss-of-function. A method which accounts for these subclasses could improve performance while also suggesting a mechanism of action for new putative cancer genes. RESULTS: We develop a panel of five complementary statistical tests and assess their performance against a curated set of 99 HiConf cancer genes using a pan-cancer dataset of 1.7 million mutations. We identify patient bias as a novel signal for cancer gene discovery, and use it to significantly improve detection of oncogenes over existing methods (AUROC = 0.894). Additionally, our test of truncation event rate separates oncogenes and TSGs from one another (AUROC = 0.922). Finally, a random forest integrating the five tests further improves performance and identifies new cancer genes, including CACNG3, HDAC2, HIST1H1E, NXF1, GPS2 and HLA-DRB1. AVAILABILITY AND IMPLEMENTATION: All mutation data, instructions, functions for computing the statistics and integrating them, as well as the HiConf gene panel, are available at www.github.com/Bose-Lab/Improved-Detection-of-Cancer-Genes. CONTACT: rbose@dom.wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Brain abscesses, neutropenia, and B-ALL: Multiple testing modalities required to confirm PDCD10 and ETV6 dual diagnoses.

Recognition of patients with multiple diagnoses, and the unique challenges they pose to clinicians and laboratorians, is increasing rapidly as genome-wide genetic testing grows in prevalence. We describe a unique patient with dual diagnoses of PDCD10-related cerebral cavernous malformations and ETV6-related thrombocytopenia with associated neutropenia. She presented with brain abscesses as an infant, which is highly atypical for these disorders in isolation. Confirming her diagnoses depended on thorough phenotyping both during and after her acute illness. Furthermore, the causative variant in ETV6 is a novel single-exon deletion that required multiple modalities with manual review to confirm, including unique use of polymorphic nucleotides in trio exome data. She illustrates the special challenges of patients with multiple diagnoses, and the multiple tools clinicians and laboratorians must use to treat them.

Selection for or against escape from nonsense mediated decay is a novel signature for the detection of cancer genes.

Escape from nonsense mediated mRNA decay (NMD-) can produce activated or inactivated gene products, and bias in rates of escape can identify functionally important genes in germline disease. We hypothesized that the same would be true of cancer genes, and tested for NMD- bias within The Cancer Genome Atlas pan-cancer somatic mutation dataset. We identify 29 genes that show significantly elevated or suppressed rates of NMD-. This novel approach to cancer gene discovery reveals genes not previously cataloged as potentially tumorigenic, and identifies many potential driver mutations in known cancer genes for functional characterization.

A deep intronic variant is a common cause of OTC deficiency in individuals with previously negative genetic testing.

Pathogenic variants in non-coding regions of genes encoding enzymes or transporters of the urea cycle can lead to urea cycle disorders (UCDs). However, not all commercially available testing platforms interrogate these regions. Here, we used a gene panel based on massively parallel sequencing (MPS) in 10 individuals with clinical or pedigree-based evidence of a proximal UCD but without a molecular confirmation of the diagnosis. We identified causal variant(s) in 5 of 10 individuals, including in 3 of 7 individuals in whom prior molecular testing was unrevealing. We show that a deep-intronic pathogenic variant in OTC, c.540+265G>A, is an important cause of ornithine transcarbamylase (OTC) deficiency.

Analysis of somatic mutations across the kinome reveals loss-of-function mutations in multiple cancer types.

In this study we use somatic cancer mutations to identify important functional residues within sets of related genes. We focus on protein kinases, a superfamily of phosphotransferases that share homologous sequences and structural motifs and have many connections to cancer. We develop several statistical tests for identifying Significantly Mutated Positions (SMPs), which are positions in an alignment with mutations that show signs of selection. We apply our methods to 21,917 mutations that map to the alignment of human kinases and identify 23 SMPs. SMPs occur throughout the alignment, with many in the important A-loop region, and others spread between the N and C lobes of the kinase domain. Since mutations are pooled across the superfamily, these positions may be important to many protein kinases. We select eleven mutations from these positions for functional validation. All eleven mutations cause a reduction or loss of function in the affected kinase. The tested mutations are from four genes, including two tumor suppressors (TGFBR1 and CHEK2) and two oncogenes (KDR and ERBB2). They also represent multiple cancer types, and include both recurrent and non-recurrent events. Many of these mutations warrant further investigation as potential cancer drivers.

Unsupervised detection of cancer driver mutations with parsimony-guided learning.

Methods are needed to reliably prioritize biologically active driver mutations over inactive passengers in high-throughput sequencing cancer data sets. We present ParsSNP, an unsupervised functional impact predictor that is guided by parsimony. ParsSNP uses an expectation-maximization framework to find mutations that explain tumor incidence broadly, without using predefined training labels that can introduce biases. We compare ParsSNP to five existing tools (CanDrA, CHASM, FATHMM Cancer, TransFIC, and Condel) across five distinct benchmarks. ParsSNP outperformed the existing tools in 24 of 25 comparisons. To investigate the real-world benefit of these improvements, we applied ParsSNP to an independent data set of 30 patients with diffuse-type gastric cancer. ParsSNP identified many known and likely driver mutations that other methods did not detect, including truncation mutations in known tumor suppressors and the recurrent driver substitution RHOA p.Tyr42Cys. In conclusion, ParsSNP uses an innovative, parsimony-based approach to prioritize cancer driver mutations and provides dramatic improvements over existing methods.

Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data.

A major goal of cancer genome sequencing is to identify mutations or other somatic alterations that can be targeted by selective and specific drugs. dGene is an annotation tool designed to rapidly identify genes belonging to one of ten druggable classes that are frequently targeted in cancer drug development. These classes were comprehensively populated by combining and manually curating data from multiple specialized and general databases. dGene was used by The Cancer Genome Atlas squamous cell lung cancer project, and here we further demonstrate its utility using recently released breast cancer genome sequencing data. dGene is designed to be usable by any cancer researcher without the need for support from a bioinformatics specialist. A full description of dGene and options for its implementation are provided here.