Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype.

Biallelic germline mutations affecting NTHL1 predispose carriers to adenomatous polyposis and colorectal cancer, but the complete phenotype is unknown. We describe 29 individuals carrying biallelic germline NTHL1 mutations from 17 families, of which 26 developed one (n = 10) or multiple (n = 16) malignancies in 14 different tissues. An unexpected high breast cancer incidence was observed in female carriers (60%). Mutational signature analysis of 14 tumors from 7 organs revealed that NTHL1 deficiency underlies the main mutational process in all but one of the tumors (93%). These results reveal NTHL1 as a multi-tumor predisposition gene with a high lifetime risk for extracolonic cancers and a typical mutational signature observed across tumor types, which can assist in the recognition of this syndrome.

The role of genetic counsellors in genomic healthcare in the United Kingdom: a statement by the Association of Genetic Nurses and Counsellors.

In the United Kingdom, genetic counsellors work together with clinical geneticists and clinical scientist colleagues within specialist genetics services, but they also often work in multidisciplinary teams (MDTs) outside of such services. There, they contribute genetic knowledge together with expert understanding of how to communicate genetic information effectively. They can offer education and support to the MDT, while providing management advice for both affected patients and the extended at-risk family members. As genomic technologies are implemented across many disciplines within healthcare, genetic counsellors are playing a key role in enabling non-genetic health professionals learn, understand and integrate genomic data into their practice. They are also involved in curriculum development, workforce planning, research, regulation and policy creation - all with the aim of ensuring a robust evidence base from which to practise, together with clear guidelines on what constitutes competence and good practice. The Association of Genetic Nurses and Counsellors (AGNC) in The United Kingdom (UK) and Republic of Ireland is committed to supporting genetic counsellors, across all sectors of healthcare and research, as they help deliver genomic medicine for the patient, family and world-class health services.European Journal of Human Genetics advance online publication, 22 March 2017; doi:10.1038/ejhg.2017.28.

Mutations in ZIC2 in human holoprosencephaly: description of a novel ZIC2 specific phenotype and comprehensive analysis of 157 individuals.

BACKGROUND: Holoprosencephaly (HPE), the most common malformation of the human forebrain, may be due to mutations in genes associated with non-syndromic HPE. Mutations in ZIC2, located on chromosome 13q32, are a common cause of non-syndromic, non-chromosomal HPE. OBJECTIVE: To characterise genetic and clinical findings in patients with ZIC2 mutations. METHODS: Through the National Institutes of Health and collaborating centres, DNA from approximately 1200 individuals with HPE spectrum disorders was analysed for sequence variations in ZIC2. Clinical details were examined and all other known cases of mutations in ZIC2 were included through a literature search. RESULTS: By direct sequencing of DNA samples of an unselected group of unrelated patients with HPE in our NIH laboratory, ZIC2 mutations were found in 8.4% (49/582) of probands. A total of 157 individuals from 119 unrelated kindreds are described, including 141 patients with intragenic sequence determined mutations in ZIC2. Only 39/157 patients have previously been clinically described. Unlike HPE due to mutations in other genes, most mutations occur de novo and the distribution of HPE types differs significantly from that of non-ZIC2 related HPE. Evidence is presented for the presence of a novel facial phenotype which includes bitemporal narrowing, upslanting palpebral fissures, a short nose with anteverted nares, a broad and well demarcated philtrum, and large ears. CONCLUSIONS: HPE due to ZIC2 mutations is distinct from that due to mutations in other genes. This may shed light on the mechanisms involved in formation of the forebrain and face and will help direct genetic counselling and diagnostic strategies.

A novel PCR approach for prenatal detection of the common NEMO rearrangement in incontinentia pigmenti.

OBJECTIVES: Incontinentia pigmenti (IP) is a rare X-linked dominant genodermatosis that is usually lethal in males in the prenatal period. Largely 80% of cases are accounted for by a large-scale deletion encompassing exons 4 to 10 of the NEMO gene. The aim of this work was to facilitate prenatal diagnosis of IP by devising a novel test for detection of the prevalent NEMO deletion. METHODS: We devised a sensitive and reproducible multiplex PCR test enabling simultaneous amplification of the deleted and wild-type NEMO genes in IP female individuals. RESULTS: Combination of this DNA test, with Xq28 linkage analysis and X-inactivation pattern study enabled us to offer an IP prenatal diagnosis in 15 of the 16 couples at a 50% risk to have an affected offspring. CONCLUSION: A current approach to IP prenatal diagnosis is proposed on the basis of the previously mentioned molecular tools.

Pilot morpholino screen in Xenopus tropicalis identifies a novel gene involved in head development.

The diploid frog X. tropicalis has recently been adopted as a model genetic system, but loss-of-function screens in Xenopus have not yet been performed. We have undertaken a pilot functional knockdown screen in X. tropicalis for genes involved in nervous system development by injecting antisense morpholino (MO) oligos directed against X. tropicalis mRNAs. Twenty-six genes with primary expression in the nervous system were selected as targets based on an expression screen previously conducted in X. laevis. Reproducible phenotypes were observed for six and for four of these, a second MO gave a similar result. One of these genes encodes a novel protein with previously unknown function. Knocking down this gene, designated pinhead, results in severe microcephaly, whereas, overexpression results in macrocephaly. Together with the early embryonic expression in the anterior neural plate, these data indicate that pinhead is a novel gene involved in controlling head development.

Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28.

A large portion of human Xq28 has been completely characterized but the interval between G6PD and Xqter has remained poorly understood. Because of a lack of stable, high-density clone coverage in this region, we constructed a 1.6-Mb bacterial and P1 artificial chromosome (BAC and PAC, respectively) contig to expedite mapping, structural and evolutionary analysis, and sequencing. The contig helped to reposition previously mismapped genes and to characterize the XAP135 pseudogene near the int22h-2 repeat. BAC clones containing the distal int22h repeats also demonstrated spontaneous rearrangements and sparse coverage, which suggested that they were unstable. Because the int22h repeats are involved in genetic diseases, we examined them in great apes to see if they have always been unstable. Differences in copy number among the apes, due to duplications and deletions, indicated that they have been unstable throughout their evolution. Taking another approach toward understanding the genomic nature of distal Xq28, we examined the homologous mouse region and found an evolutionary junction near the distal int22h loci that separated the human distal Xq28 region into two segments on the mouse X chromosome. Finally, haplotype analysis showed that a segment within Xq28 has resisted excessive interchromosomal exchange through great ape evolution, potentially accounting for the linkage disequilibrium recently reported in this region. Collectively, these data highlight some interesting features of the genomic sequence in Xq28 and will be useful for positional cloning efforts, mouse mutagenesis studies, and further evolutionary analyses.

Disease-associated mutations in L1 CAM interfere with ligand interactions and cell-surface expression.

Mutations in the L1CAM gene cause a highly variable neurological disease described as X-linked hydrocephalus, MASA syndrome or spastic paraplegia type I. Over one-third of the mutations identified in affected boys are missense, unique to individual families and distributed primarily across the large extracellular domain of the L1 protein. We have examined the effects of 25 missense mutations on binding to homophilic (L1) and heterophilic (TAX-1) ligands as well as on intracellular trafficking. All but three of these result in reduced ligand binding or impaired movement to the surface of COS and CHO cells. Therefore, we demonstrate for the first time that most missense mutations found in affected families have functional consequences. Furthermore, mutations that are predicted to affect the structure of individual extracellular domains are more likely to affect intracellular processing and/or ligand binding than those mutations affecting surface properties of the molecule.