Challenges and opportunities for effective delivery of clinical genetic services in the U.S. healthcare system.

PURPOSE OF REVIEW: Demand for clinical genetics and genomics services is increasing. As discussed in this study, the clinical genetics and genomics workforce is small. How to meet the demand with a limited workforce requires innovation. RECENT FINDINGS: Background data regarding the current state of clinical genetic services including volume of services and make-up of the clinical genetics workforce are presented. The study then identifies opportunities to increase access to clinical genetic service providers using new models of service and discusses examples of solutions which have been implemented in some practice settings. Creative uses of technology to increase providers' efficiency are highlighted. SUMMARY: Clinical genetics service providers need to rise to the occasion and lead the transformation of clinical genetic service delivery. Many of the examples of solutions described in the study can be implemented by other providers now. Additionally, the described solutions may serve to inspire genetic providers to create their own new solutions, which should then be shared with the provider community.

Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats.

We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers.

Fine mapping of breakpoints in two unrelated patients with rare overlapping interstitial deletions of 9q with mild dysmorphic features.

Approximately, 20 cases of interstitial deletions of 9q have been reported in the literature spanning the breakpoints from 9q21 to 9q34. Unlike the 9q subtelomeric deletions, the interstitial deletions do not demonstrate a specific recognizable phenotype, although the majority of patients had microcephaly. Lack of precise molecular delineation of the extent of deletions in the published cases makes it difficult to develop an accurate genotype-phenotype correlation. We report on fine mapping of breakpoints using the Affymetrix Human Mapping 500K Array Set in two unrelated female patients with overlapping de novo deletion in 9q. SNP oligonucleotide microarray analysis (SOMA) indicated these to be relatively large deletions with Patient 1 having a 6.47 Mb deletion (>60 genes) spanning 9q32-q33.2 and Patient 2 having a 9.68 Mb deletion (>20 genes) localized to 9q31.1-q33.1. FISH analysis with BAC clones localized to the breakpoints showed discrepant results in Patient 1. Based on the review of previously reported interstitial 9q deletion patients and our patients, the minimal region of overlap (MRO) appears to encompass the 9q32 region and a phenotype characterized by microcephaly, neurological dysfunction and facial dysmorphism can be deduced. Our study shows the investigative nature of the latest array technology and the limitations of this technology in the accurate delineation of breakpoints.

Unusual mosaic karyotype resulting from adjacent 1 segregation of t(11;22): importance of performing skin fibroblast karyotype in patients with unexplained multiple congenital anomalies.

We report a patient with a mosaic karyotype resulting from an adjacent 1 segregation of the familial autosomal translocation (11;22). The karyotype seen in fibroblast is 46,XY,der(22)t(11;22)(q23.3;q11.2)/46,XY. No evidence of the abnormal cell line was seen in the cultures obtained from the lymphocytes. The clinical phenotype of the patient does not fit a particular pattern of partial monosomy 22 or partial trisomy 11. There are some features that have been previously reported in patients with trisomy 11q23 --> qter. The mosaic karyotype in our patient could be a result of a series of postzygotic mitotic events of a zygote carrying the der(22) chromosome. These mechanisms involve events that are well documented for several chromosomes. This case underscores the necessity of performing exhaustive cytogenetic analysis in patients with an abnormal phenotype with a family history of a chromosome rearrangement in fibroblast cells if lymphocyte analysis is normal.

Molecular and clinical analyses of Greig cephalopolysyndactyly and Pallister-Hall syndromes: robust phenotype prediction from the type and position of GLI3 mutations.

Mutations in the GLI3 zinc-finger transcription factor gene cause Greig cephalopolysyndactyly syndrome (GCPS) and Pallister-Hall syndrome (PHS), which are variable but distinct clinical entities. We hypothesized that GLI3 mutations that predict a truncated functional repressor protein cause PHS and that functional haploinsufficiency of GLI3 causes GCPS. To test these hypotheses, we screened patients with PHS and GCPS for GLI3 mutations. The patient group consisted of 135 individuals: 89 patients with GCPS and 46 patients with PHS. We detected 47 pathological mutations (among 60 probands); when these were combined with previously published mutations, two genotype-phenotype correlations were evident. First, GCPS was caused by many types of alterations, including translocations, large deletions, exonic deletions and duplications, small in-frame deletions, and missense, frameshift/nonsense, and splicing mutations. In contrast, PHS was caused only by frameshift/nonsense and splicing mutations. Second, among the frameshift/nonsense mutations, there was a clear genotype-phenotype correlation. Mutations in the first third of the gene (from open reading frame [ORF] nucleotides [nt] 1-1997) caused GCPS, and mutations in the second third of the gene (from ORF nt 1998-3481) caused primarily PHS. Surprisingly, there were 12 mutations in patients with GCPS in the 3' third of the gene (after ORF nt 3481), and no patients with PHS had mutations in this region. These results demonstrate a robust correlation of genotype and phenotype for GLI3 mutations and strongly support the hypothesis that these two allelic disorders have distinct modes of pathogenesis.