SA Clinical Genetics Service

Adelaide, Australia

SA Clinical Genetics Service

Adelaide, Australia

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Bennetts B.,The Childrens Hospital at Westmead | Caramins M.,SDS Pathology | Hsu A.,University of Melbourne | Lau C.,Albion College | And 10 more authors.
Applied and Translational Genomics | Year: 2014

Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA) in collaboration with the Human Genetics Society of Australasia (HGSA), and the Human Variome Project (HVP) is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions. © 2014.


Ruggieri A.,Fondazione Irccs Instituto Neurologico C Besta | Ruggieri A.,University of Toronto | Ramachandran N.,University of Toronto | Wang P.,University of Toronto | And 10 more authors.
Neuromuscular Disorders | Year: 2015

X-linked Myopathy with Excessive Autophagy (XMEA) affects proximal muscles of the lower extremities and follows a progressive course reminiscent of muscular dystrophy. It is caused by mutations in VMA21 whose protein product assembles lysosomes' proton pumps. All XMEA mutations to date have been single-nucleotide substitutions that reduce VMA21 expression, which leads to modest lysosomal pH increase, the first step in the disease's pathogenesis. We now report a new class of XMEA mutations. We identified two VMA21 non-coding microdeletions, one intronic (c.54-16_54-8del), the other in the 3'UTR (c.*13_*104del). Both resulted in a relatively more severe (early ambulation loss), diffuse (extra-ocular and upper extremity involvement), and early (neonatal) onset disease compared to previously reported patients. Our cases highlight the importance of including non-coding regions of VMA21 in genetic testing panels of dystrophies and myopathies. Specific diagnosis of XMEA will be particularly important as therapies aimed at correcting the modest rise in lysosomal pH at the root of this disease are developed. © 2014 Elsevier B.V.


Lewinsohn M.,University of Chicago | Brown A.L.,SA Pathology | Brown A.L.,Center for Cancer Biology | Brown A.L.,University of South Australia | And 41 more authors.
Blood | Year: 2016

Recently our group and others have identified DDX41 mutations both as germ line and acquired somatic mutations in families with multiple cases of late onset myelodysplastic syndrome (MDS) and/or acute myeloid leukemia (AML), suggesting that DDX41 acts as a tumor suppressor. To determine whether novel DDX41 mutations could be identified in families with additional types of hematologic malignancies, our group screened two cohorts of families with a diverse range of hematologic malignancy subtypes. Among 289 families, we identified nine (3%) with DDX41 mutations. As previously observed, MDS and AML were the most common malignancies, often of the erythroblastic subtype, and 1 family displayed early-onset follicular lymphoma. Five novelmutations were identified, including missensemutations within important functional domains and start-loss and splicingmutations predicted to result in truncated proteins.We also show that most asymptomatic mutation carriers have normal blood counts until malignancy develops. This study expands both the mutation and phenotypic spectra observed in families with germ line DDX41 mutations. With an increasing number of both inheritedand acquiredmutations in thisgene being identified, further studyof howDDX41 disruption leads to hematologicmalignancies is critical. © 2016 by The American Society of Hematology.


Hahn C.N.,Center for Cancer Biology | Hahn C.N.,University of Adelaide | Chong C.-E.,Center for Cancer Biology | Chong C.-E.,University of Adelaide | And 37 more authors.
Nature Genetics | Year: 2011

We report the discovery of GATA2 as a new myelodysplastic syndrome (MDS)-acute myeloid leukemia (AML) predisposition gene. We found the same, previously unidentified heterozygous c.1061C>T (p.Thr354Met) missense mutation in the GATA2 transcription factor gene segregating with the multigenerational transmission of MDS-AML in three families and a GATA2 c.1063-1065delACA (p.Thr355del) mutation at an adjacent codon in a fourth MDS family. The resulting alterations reside within the second zinc finger of GATA2, which mediates DNA-binding and protein-protein interactions. We show differential effects of the mutations on the transactivation of target genes, cellular differentiation, apoptosis and global gene expression. Identification of such predisposing genes to familial forms of MDS and AML is critical for more effective diagnosis and prognosis, counseling, selection of related bone marrow transplant donors and development of therapies. © 2011 Nature America, Inc. All rights reserved.


Howard H.J.,Florey Neurosciences Institute | Beaudet A.,Baylor College of Medicine | Gil-da-Silva Lopes V.,University of Campinas | Lyne M.,University of Cambridge | And 5 more authors.
American Journal of Medical Genetics, Part A | Year: 2012

The need for Locus-Specific Databases, with disease-specific experts and curators, is an essential ingredient in a process to enable the benefits of the advances in sequencing and mutational analysis to be realized across the genome. Next generation sequencing provides both astounding opportunities and challenges, especially for genetic counsellors. An approach coordinated at a genome wide, international level, supported by well-organized disease-specific respected organizations is a model most likely to be successful, but committed resourceful professionals working in local poorly resourced environments can make valuable contributions that can grow. Bioinformatic tools to sift and integrate multiple domains of information are being developed, and play a major part in meeting the challenges. Regulation of providers, including a requirement for them to submit mutational information to central databases, also should assist to reach the goals needed to realize the opportunities. There is also a need to agree on governance of Locus-Specific Databases (LSDBs) at an international level, and for adequate international funding to support this need, to ensure humanity reaps the benefits of the current molecular genetic revolution. The Human Variome Project offers this, working also with the other major initiatives with similar objectives. This report concludes with Recommendations for the Human Variome Project stemming from the presentations and discussions at the meeting. © 2012 Wiley Periodicals, Inc.


PubMed | University of Washington, University of Chicago, Stanford University, Center for Cancer Biology and 5 more.
Type: Journal Article | Journal: Blood | Year: 2016

Recently our group and others have identified DDX41 mutations both as germ line and acquired somatic mutations in families with multiple cases of late onset myelodysplastic syndrome (MDS) and/or acute myeloid leukemia (AML), suggesting that DDX41 acts as a tumor suppressor. To determine whether novel DDX41 mutations could be identified in families with additional types of hematologic malignancies, our group screened two cohorts of families with a diverse range of hematologic malignancy subtypes. Among 289 families, we identified nine (3%) with DDX41 mutations. As previously observed, MDS and AML were the most common malignancies, often of the erythroblastic subtype, and 1 family displayed early-onset follicular lymphoma. Five novel mutations were identified, including missense mutations within important functional domains and start-loss and splicing mutations predicted to result in truncated proteins. We also show that most asymptomatic mutation carriers have normal blood counts until malignancy develops. This study expands both the mutation and phenotypic spectra observed in families with germ line DDX41 mutations. With an increasing number of both inherited and acquired mutations in this gene being identified, further study of how DDX41 disruption leads to hematologic malignancies is critical.

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