Changing interpretation of chromosomal microarray over time in a community cohort with intellectual disability.

Chromosomal microarray (CMA) is the first-line diagnostic test for individuals with intellectual disability, autism, or multiple congenital anomalies, with a 10-20% diagnostic yield. An ongoing challenge for the clinician and laboratory scientist is the interpretation of variants of uncertain significance (VOUS)-usually rare, unreported genetic variants. Laboratories differ in their threshold for reporting VOUS, and clinical practice varies in how this information is conveyed to the family and what follow-up is arranged. Workflows, websites, and databases are constantly being updated to aid the interpretation of VOUS. There is a growing literature reporting new microdeletion and duplication syndromes, susceptibility, and modifier copy number variants (CNVs). Diagnostic methods are also evolving with new array platforms and genome builds. In 2010, high-resolution arrays (Affymetrix 2.7 M Oligo and SNP, 50 kB resolution) were performed on a community cohort of 67 individuals with intellectual disability of unknown aetiology. Three hundred and one CNVs were detected and analyzed using contemporary resources and a simple scoring system. Thirteen (19%) of the arrays were assessed as potentially pathogenic, 4 (6%) as benign and 50 (75%) of uncertain clinical significance. The CNV data were re-analyzed in 2012 using the contemporary interpretative resources. There was a statistically significant difference in the assessment of individual CNVs (P < 0.0001). An additional eight patients were reassessed as having a potentially pathogenic array (n = 21, 31%) and several additional susceptibility or modifier CNVs were identified. This study highlights the complexity involved in the interpretation of CMA and uniquely demonstrates how, even on the same array platform, it can be subject to change over time.

A comparison of molecular and cytogenetic techniques for the diagnosis of pregnancy loss.

PURPOSE: To evaluate the sensitivity, specificity, advantages, and limitations of multiplex ligation-dependent probe amplification compared with conventional karyotype analysis in the investigation of contributing factors to recurrent pregnancy loss. METHOD: A cohort of 284 patients underwent side-by-side analysis of products of conception by both conventional karyotyping and multiplex ligation-dependent probe amplification with direct comparison of results. RESULTS: Multiplex ligation-dependent probe amplification was shown to enable a diagnosis for an additional 47 (16.5%) patients compared with conventional karyotype analysis. However, this advantage was offset by some disadvantages of the method, including a high false-positive rate (8/104; 7.7%), as demonstrated by single-arm probe abnormalities of uncertain clinical significance, as well as the inability to characterize structural rearrangements, such as Robertsonian translocations, which comprised 2.46% of samples (99% confidence interval = 0.09-4.83), and ploidy changes. The calculated performance characteristics of multiplex ligation-dependent probe amplification in this cohort yielded a sensitivity of 86.9% and specificity of 92.4%. CONCLUSIONS: The advantages of now widely accepted molecular methodologies, such as lower failure rates, faster turnaround times, and lower cost, must be complemented by adequate counseling, family follow-up, and specific diagnostic reporting practices. It is particularly important to specifically address the important limitations of the methodology, including the inability to characterize balanced structural rearrangements and ploidy changes, especially if multiplex ligation-dependent probe amplification is to be performed alone.

Breast cancer risk is not increased in individuals with TWIST1 mutation confirmed Saethre-Chotzen syndrome: an Australian multicenter study.

Saethre-Chotzen syndrome (SCS) is a rare autosomal dominant syndrome involving craniosynostosis, craniofacial abnormalities, and syndactyly. A recent Scandinavian study reported an increased risk of breast cancer in individuals with a clinical diagnosis of SCS. Because of the potential importance of this finding, we organized a multicenter study enrolling people with TWIST1 mutation confirmed SCS to determine if an increased risk of cancer is present. This study did not identify any cases of breast or ovarian cancer in a cohort of equivalent power to that reported previously. These results provide clinical reassurance that at present there is no evidence for breast cancer screening above standard practice for individuals with SCS.

Measurement of the clinical utility of a combined mutation detection protocol in carriers of Duchenne and Becker muscular dystrophy.

BACKGROUND: Recent methodological advances have improved the detection rate for dystrophin mutations, but there are no published studies that have measured the clinical utility of these protocols for carrier detection compared with conventional carrier testing protocols that use pedigree, serum creatine kinase levels and linkage analysis. METHODS AND SUBJECTS: The clinical utility of a combined mutation detection protocol was measured. It involved quantitative PCR procedures followed by DNA sequence analysis for the identification of dystrophin mutation carriers in 2101 women at risk of being carriers from 348 mutation-known Duchenne or Becker muscular dystrophy pedigrees. RESULTS: The combined mutation detection protocol identified a mutation in 96% and 82% of index cases of Duchenne muscular dystrophy and Becker muscular dystrophy, respectively. An additional 692 (33%) potential carriers were correctly classified by the combined mutation detection protocol compared with pedigree, serum creatine kinase levels and linkage analysis. Significantly lower mutation carrier rates were identified in the mothers of isolated cases with deletion mutations than predicted from theoretical considerations, but these findings were not confirmed for duplication and DNA sequence mutations. CONCLUSIONS: There are significant clinical benefits to be gained from a combined mutation detection protocol for carrier detection. It is recommended that mutation-specific carrier frequencies for the different classes of dystrophin mutations should be taken into account in genetic counselling practice.

Mutations in the gene encoding the PML nuclear body protein Sp110 are associated with immunodeficiency and hepatic veno-occlusive disease.

We describe mutations in the PML nuclear body protein Sp110 in the syndrome veno-occlusive disease with immunodeficiency, an autosomal recessive disorder of severe hypogammaglobulinemia, combined T and B cell immunodeficiency, absent lymph node germinal centers, absent tissue plasma cells and hepatic veno-occlusive disease. This is the first report of the involvement of a nuclear body protein in a human primary immunodeficiency and of high-penetrance genetic mutations in hepatic veno-occlusive disease.