BackgroundExon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype–phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery.MethodsWe retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association.ResultsIn this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses.ConclusionsTogether, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-017-0472-7) contains supplementary material, which is available to authorized users.

Summary Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated ( DVL1 , DVL3 , FZD2 , NXN , ROR2 , and WNT5A ). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in DVL2 . We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with FZD2 variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic NXN variants clustered together with the majority of probands carrying DVL1 , DVL2 , and DVL3 variants, demonstrating no phenotypic distinction between the NXN -autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing WNT5A , FZD2 , and ROR2 apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.

Neurofibromatosis Type 1 (NF1) is a progressive genetic disorder characterized by physical findings such as café-au-lait macules, Lisch nodules, and neurofibromas in addition to other medical complications. Learning and social problems are more prevalent among individuals affected with NF1. It has been reported that people with NF1 have lower self-esteem (SE) when compared to the general population. Additionally, a study published over 20 years ago found that overall knowledge of NF1 was lacking in individuals affected with the condition. The goals of our study were to evaluate NF1 knowledge in adolescents and adults with the condition, as well as to determine if there is a link between patient knowledge and SE. Furthermore, we explored the impact of other factors, such as attendance at a NF1 support group and having a family history of NF1, on knowledge and SE. A survey comprised of knowledge-based questions and the Rosenberg Self-Esteem Scale was distributed to individuals with NF1 through the Texas NF Foundation. Overall, the 49 respondents (13 to 73 years of age) had a mean knowledge score of 77.9 % correct answers. Consistent with previous studies, the SE of our study population was lower when compared to general population norms. Although no correlation between knowledge and SE was observed, SE scores were on average higher if a person reported the following: having friends with NF1 (p = 0.009); attending a NF1 support group (p = 0.006); receiving care at a NF clinic (p = 0.049); or having received genetic counseling (p = 0.008). Further research is needed to better understand the relationship between these factors and SE in the NF1 population.

Pakistan is a densely populated country in South Asia with a high burden of genetic disease. A dearth of medical genetic services exists and master's level trained genetic counselors (GCs) are currently not a part of the healthcare system. This study is the first to determine the views of Pakistani medical doctors (MDs) towards genetic counseling services in Pakistan, including what manner a master's level genetic counselor might be incorporated into the healthcare system. Fifty-one MDs practicing in the city of Karachi completed a self-administered survey of twenty questions. Of the 49 respondents who answered a specific question, 100 % (49/49) felt that they would refer at least some, if not all, of their relevant patients to a genetic's clinic if one existed in Karachi. Overall, the respondents showed a positive attitude towards the provision of genetic counseling services as a part of the healthcare system of Pakistan. Some of the proposed roles identified specifically for GCs included: explaining how Down syndrome occurs (66.1 %), discussing genes associated with breast cancer (77.4 %), and explaining the inheritance pattern of β-thalassemia (65.5 %). In contrast, the review of medical and family history and discussion of medical procedures such as ultrasound and amniocentesis were typically seen as the role of a physician. A majority of the respondents (98 %) were in favor of premarital carrier screening for thalassemia and would refer patients to a GC to describe the importance of carrier screening (84.3 %) and to help explain carrier screening results (94.1 %). Many respondents selected GCs as the ideal provider of education and support for people with inherited conditions (43.8 %), followed by specialist MDs (26 %) and general physicians (22.9 %). Considering the high burden of genetic disease in the country, we encourage the development of genetic counseling services in Pakistan.