An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Additional file 1: Figure S1A. of A patient with van Maldergem syndrome with endocrine abnormalities, hypogonadotropic hypogonadism, and breast aplasia/hypoplasia

Pathways of estrogen activation of gene transcription (Classic): E2 = Estradiol, ER = Estrogen Receptor, ERE = Estrogen Receptor Elements. Estrogen (estradiol, E2) is the major factor in promoting breast development by activating the estrogen receptor Îą (ESR1) but there are different pathways; the classic genomic pathway and alternatives. In the classic pathway (Figure S1, A), the activated ESR1 dimerizes, binds with high affinity and specificity to DNA sequences called estrogen response elements (EREs) to regulate transcription rates of target genes. Activated ESR1 then recruits-interacts with steroid receptor co-regulators (SRCS) and chromatin remodelers that facilitate access to chromatin and coordinate transcription of the transcriptional modulators. Transcription is facilitated or impeded in part by modifications of histones, the more abundant proteins in the nucleus which package the DNA. Modification of histones by acetylation via histone acetyl transferases or deacetylation via histone deacetylases affects transcription of genes [22]. Figure S1B. There are alternative mechanisms of action when the estrogen receptor can sometimes regulate expression of genes that lack EREs resulting in activation of reporter genes containing activator protein 1 (Ap-1) elements (Figure S1, B). Through protein-protein interaction, estrogen receptors can modulate the transcriptional activity of heterodimers of the transcription factors fos and jun (Ap-1 responsive elements), leading to activation of reporter genes containing Ap-1 elements. This non-classical genomic pathway is also functional in vivo. Ap-1 is a transcription factor complex containing the proto-oncogenes jun/fos and other family members. This complex interacts with Ap-1 sites in gene promoters to activate a large number of genes involved in cellular differentiation and development [16]. (DOCX 96 kb

Somatic PIK3R1 variation as a cause of vascular malformations and overgrowth.

PurposeSomatic activating variants in the PI3K-AKT pathway cause vascular malformations with and without overgrowth. We previously reported an individual with capillary and lymphatic malformation harboring a pathogenic somatic variant in PIK3R1, which encodes three PI3K complex regulatory subunits. Here, we investigate PIK3R1 in a large cohort with vascular anomalies and identify an additional 16 individuals with somatic mosaic variants in PIK3R1.MethodsAffected tissue from individuals with vascular lesions and overgrowth recruited from a multisite collaborative network was studied. Next-generation sequencing targeting coding regions of cell-signaling and cancer-associated genes was performed followed by assessment of variant pathogenicity.ResultsThe phenotypic and variant spectrum associated with somatic variation in PIK3R1 is reported herein. Variants occurred in the inter-SH2 or N-terminal SH2 domains of all three PIK3R1 protein products. Phenotypic features overlapped those of the PIK3CA-related overgrowth spectrum (PROS). These overlapping features included mixed vascular malformations, sandal toe gap deformity with macrodactyly, lymphatic malformations, venous ectasias, and overgrowth of soft tissue or bone.ConclusionSomatic PIK3R1 variants sharing attributes with cancer-associated variants cause complex vascular malformations and overgrowth. The PIK3R1-associated phenotypic spectrum overlaps with PROS. These data extend understanding of the diverse phenotypic spectrum attributable to genetic variation in the PI3K-AKT pathway