Socioeconomic status and uptake of reproductive carrier screening in Australia.

Reproductive carrier screening enables the early identification of genetic conditions that may impact the long-term health of a child, including cystic fibrosis, fragile X syndrome, and spinal muscular atrophy. We used unique data from the major providers of pathology services in Australia to profile women who intend on becoming, or who are, pregnant and access basic to advanced testing for genetic conditions. We found a strong socioeconomic gradient in the uptake of reproductive carrier screening, with women living in the most advantaged postcodes across Australia significantly being more likely to have reproductive carrier screening than those living in the most disadvantaged areas. These results highlight the need to minimise social and financial barriers that are currently limiting access.

Exome sequencing identification of a GJB1 missense mutation in a kindred with X-linked spinocerebellar ataxia (SCA-X1).

We undertook a gene identification and molecular characterization project in a large kindred originally clinically diagnosed with SCA-X1. While presenting with ataxia, this kindred also had some unique peripheral nervous system features. The implicated region on the X chromosome was delineated using haplotyping. Large deletions and duplications were excluded by array comparative genomic hybridization. Exome sequencing was undertaken in two affected subjects. The single identified X chromosome candidate variant was then confirmed to co-segregate appropriately in all affected, carrier and unaffected family members by Sanger sequencing. The variant was confirmed to be novel by comparison with dbSNP, and filtering for a minor allele frequency of <1% in 1000 Genomes project, and was not present in the NHLBI Exome Sequencing Project or a local database at the BCM HGSC. Functional experiments on transfected cells were subsequently undertaken to assess the biological effect of the variant in vitro. The variant identified consisted of a previously unidentified non-synonymous variant, GJB1 p.P58S, in the Connexin 32/Gap Junction Beta 1 gene. Segregation studies with Sanger sequencing confirmed the presence of the variant in all affected individuals and one known carrier, and the absence of the variant in unaffected members. Functional studies confirmed that the p.P58S variant reduced the number and size of gap junction plaques, but the conductance of the gap junctions was unaffected. Two X-linked ataxias have been associated with genetic loci, with the first of these recently characterized at the molecular level. This represents the second kindred with molecular characterization of X-linked ataxia, and is the first instance of a previously unreported GJB1 mutation with a dominant and permanent ataxia phenotype, although different CNS deficits have previously been reported. This pedigree has also been relatively unique in its phenotype due to the presence of central and peripheral neural abnormalities. Other X-linked SCAs with unique features might therefore also potentially represent variable phenotypic expression of other known neurological entities.

Chronic lymphocytic leukaemia, monoclonal B-lymphocytosis and pregnancy: five cases, a literature review and discussion of management.

Chronic lymphocytic leukaemia (CLL) occurs rarely with pregnancy and monoclonal B-Lymphocytosis (MBL) has not previously been described in this setting. CLL is predominantly a disease of the elderly and affects men twice as often as women and hence only an estimated 2% of patients are females of childbearing age. We identified only five reported cases of CLL in pregnancy in the literature. We describe two additional cases, plus three other women with CLL dealing with pregnancy-related decisions. We review the literature and discuss proposals for management and issues that arise in this relatively uncommon occurrence. In contrast to many other haematological malignancies where longer remissions are typically associated with a lower risk of relapse, most patients with CLL who require treatment will ultimately relapse with current therapy. This complex setting requires careful consideration and well informed patients to assist with decisions related to pregnancy.

Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge.

Massively parallel sequencing has become a powerful tool for the clinical management of patients with applications in diagnosis, guidance of treatment, prediction of drug response, and carrier screening. A considerable challenge for the clinical implementation of these technologies is the management of the vast amount of sequence data generated, in particular the annotation and clinical interpretation of genomic variants. Here, we describe annotation steps that can be automated and common strategies employed for variant prioritization. The definition of best practice standards for variant annotation and prioritization is still ongoing; at present, there is limited consensus regarding an optimal clinical sequencing pipeline. We provide considerations to help define these. For the first time, clinical genetics and genomics is not limited by our ability to sequence, but our ability to clinically interpret and use genomic information in health management. We argue that the development of standardized variant annotation and interpretation approaches and software tools implementing these warrants further support. As we gain a better understanding of the significance of genomic variation through research, patients will be able to benefit from the full scope that these technologies offer.

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.

Challenges for clinical genetic DNA testing.

DNA testing was first used in the late 1970s. Today, the indications for a DNA test have expanded to include predicting the development of genetic disorders, screening populations, confirming clinical diagnoses, prenatal testing and DNA testing to individualize medical treatment. Apart from the wide range of indications, the next few years will see a great expansion in the number of DNA tests. This will be driven by information generated from the Human Genome Project. Improved technology will make DNA testing more accessible. In this climate, the challenges will be considerable, particularly in relation to education. The avoidance of ethical, legal and social dilemmas will require informed and wise input from professionals and the community.

Approaches for classifying DNA variants found by Sanger sequencing in a medical genetics laboratory.

Diagnostic applications of DNA sequencing technologies present a powerful tool for the clinical management of patients. Applications range from better diagnostic classification to identification of therapeutic options, prediction of drug response and toxicity, and carrier testing. Although the advent of massively parallel sequencing technologies has increased the complexity of clinical interpretation of sequence variants by an order of magnitude, the annotation and interpretation of the clinical effects of identified genomic variants remain a challenge regardless of the sequencing technologies used to identify them. Here, we survey methodologies which assist in the diagnostic classification of DNA variants and propose a practical decision analytic protocol to assist in the classification of sequencing variants in a clinical setting. The methods include database queries, software tools for protein consequence, evolutionary conservation and pathogenicity prediction, familial segregation, case-control studies, and literature review. These methods are deliberately pragmatic as diagnostic constraints of clinically useful turnaround times generally preclude obtaining evidence from in vivo or in vitro functional experiments for variant assessment. Clinical considerations require that variant classification is stringent and rigorous, as misinterpretation may lead to inappropriate clinical consequences; thus, multiple parameters and lines of evidence are considered to determine potential biological significance.

Genomics and personalised whole-of-life healthcare.

Genome sequencing has the potential for stratified cancer treatment and improved diagnostics for rare disorders. However, sequencing needs to be utilised in risk stratification on a population scale to deepen the impact on the health system by addressing common diseases, where individual genomic variants have variable penetrance and minor impact. As the accuracy of genomic risk predictors is bounded by heritability, environmental factors such as diet, lifestyle, and microbiome have to be considered. Large-scale, longitudinal research programmes need to study the intrinsic properties between both genetics and environment to unravel their risk contribution. During this discovery process, frameworks need to be established to counteract unrealistic expectations. Sufficient scientific evidence is needed to interpret sources of uncertainty and inform decision making for clinical management and personal health.