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Our Publications

A clinical evaluation tool for SNP arrays, especially for autosomal recessive conditions in offspring of consanguineous parents

Genetics in Medicine

Purpose

This report describes a fast online tool to accelerate and improve clinical interpretation of single nucleotide polymorphism array results for diagnostic purposes, when consanguinity or inbreeding is identified.

 

Methods

 

We developed a web-based program that permits entry of regions of homozygosity and, using OMIM, UCSC, and NCBI databases, retrieves genes within these regions as well as their associated autosomal recessive disorders. Relevant OMIM Clinical Synopses can be searched, using key clinical terms permitting further filtering for candidate genes and disorders.

 

Results

The tool aids the clinician by arriving at a short list of relevant candidate disorders, guiding the continued diagnostic work-up. Its efficacy is illustrated by presenting seven patients who were diagnosed using this tool.

 

Conclusion

The online single nucleotide polymorphism array evaluation tool rapidly and systematically identifies relevant genes and associated conditions mapping to identified regions of homozygosity. The built-in OMIM clinical feature search allows the user to further filter to reach a short list of candidate conditions relevant for the diagnosis, making it possible to strategize more focused diagnostic testing. The tabulated results can be downloaded and saved to the desktop in an Excel format. Its efficacy is illustrated by providing a few clinical examples.

 

Genet Med. 2013:15(5):354-360.

Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility

European Journal of Human Genetics

Copy neutral segments with allelic homozygosity, also known as regions of homozygosity (ROHs), are frequently identified in cases interrogated by oligonucleotide single-nucleotide polymorphism (oligo-SNP) microarrays. Presence of ROHs may be because of parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, consanguinity or uniparental disomy. In this study of 14 574 consecutive cases, 832 (6%) were found to harbor one or more ROHs over 10 Mb, of which 651 cases (78%) had multiple ROHs, likely because of identity by descent (IBD), and 181 cases (22%) with ROHs involving a single chromosome. Parental relatedness was predicted to be first degree or closer in 5%, second in 9% and third in 19%. Of the 181 cases, 19 had ROHs for a whole chromosome revealing uniparental isodisomy (isoUPD). In all, 25 cases had significant ROHs involving a single chromosome; 5 cases were molecularly confirmed to have a mixed iso- and heteroUPD15 and 1 case each with segmental UPD9pat and segmental UPD22mat; 17 cases were suspected to have a mixed iso- and heteroUPD including 2 cases with small supernumerary marker and 2 cases with mosaic trisomy. For chromosome 15, 12 (92%) of 13 molecularly studied cases had either Prader–Willi or Angelman syndrome. Autosomal recessive disorders were confirmed in seven of nine cases from eight families because of the finding of suspected gene within a ROH. This study demonstrates that ROHs are much more frequent than previously recognized and often reflect parental relatedness, ascertain autosomal recessive diseases or unravel UPD in many cases.

Eur J Hum Genet. 2015 May;23(5):663-71.

Other Relevant Publications in the Rare Genomic Disease Field

Congenital protein losing enteropathy: an inborn error

of lipid metabolism due to DGAT1 mutations

European Journal of Human Genetics

Protein-losing enteropathy (PLE) is a clinical disorder of protein loss from the gastrointestinal system that results in hypoproteinemia and malnutrition. This condition is associated with a wide range of gastrointestinal disorders. Recently, a unique syndrome of congenital PLE associated with biallelic mutations in the DGAT1 gene has been reported in a single family. We hypothesize that mutations in this gene are responsible for undiagnosed cases of PLE in infancy. Here we investigated three children in two families presenting with severe diarrhea, hypoalbuminemia and PLE, using clinical studies, homozygosity mapping, and exome sequencing. In one family, homozygosity mapping using SNP arrays revealed the DGAT1 gene as the best candidate gene for the proband. Sequencing of all the exons including flanking regions and promoter regions of the gene identified a novel homozygous missense variant, p.(Leu295Pro), in the highly conserved membrane-bound O-acyl transferase (MBOAT) domain of the DGAT1 protein. Expression studies verified reduced amounts of DGAT1 in patient fibroblasts. In a second family, exome sequencing identified a previously reported splice site mutation in intron 8. These cases of DGAT1 deficiency extend the molecular and phenotypic spectrum of PLE, suggesting a re-evaluation of the use of DGAT1 inhibitors for metabolic disorders including obesity and diabetes.

Eur J Hum Genet. 2016 Aug;24(9):1268-73.

Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice

Proceedings of the National Academy of Sciences of the United States of America

Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital visceral myopathy characterized by severe dilation of the urinary bladder and defective intestinal motility. The genetic basis of MMIHS has been ascribed to spontaneous and autosomal dominant mutations in actin gamma 2 (ACTG2), a smooth muscle contractile gene. However, evidence suggesting a recessive origin of the disease also exists. Using combined homozygosity mapping and whole exome sequencing, a genetically isolated family was found to carry a premature termination codon in Leiomodin1 (LMOD1), a gene preferentially expressed in vascular and visceral smooth muscle cells. Parents heterozygous for the mutation exhibited no abnormalities, but a child homozygous for the premature termination codon displayed symptoms consistent with MMIHS. We used CRISPR-Cas9 (CRISPR-associated protein) genome editing of Lmod1 to generate a similar premature termination codon. Mice homozygous for the mutation showed loss of LMOD1 protein and pathology consistent with MMIHS, including late gestation expansion of the bladder, hydronephrosis, and rapid demise after parturition. Loss of LMOD1 resulted in a reduction of filamentous actin, elongated cytoskeletal dense bodies, and impaired intestinal smooth muscle contractility. These results define LMOD1 as a disease gene for MMIHS and suggest its role in establishing normal smooth muscle cytoskeletal–contractile coupling.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2739-E2747.

Identification of a Dutch founder mutation in MUSK causing fetal akinesia deformation sequence

European Journal of Human Genetics

Fetal akinesia deformation sequence (FADS) refers to a clinically and genetically heterogeneous group of disorders with congenital malformations related to impaired fetal movement. FADS can result from mutations in CHRNG, CHRNA1, CHRND, DOK7 and RAPSN; however, these genes only account for a minority of cases. Here we identify MUSK as a novel cause of lethal FADS. Fourteen affected fetuses from a Dutch genetic isolate were traced back to common ancestors 11 generations ago. Homozygosity mapping in two fetuses revealed MUSK as a candidate gene. All tested cases carried an identical homozygous variant c.1724T4C; p.(Ile575Thr) in the intracellular domain of MUSK. The carrier frequency in the genetic isolate was 8%, exclusively found in heterozygous carriers. Consistent with the established role of MUSK as a tyrosine kinase that orchestrates neuromuscular synaptogenesis, the fetal myopathy was accompanied by impaired acetylcholine receptor clustering and reduced tyrosine kinase activity at motor nerve endings. A functional assay in myocytes derived from human fetuses confirmed that the variant blocks MUSK-dependent motor endplate formation. Taken together, the results strongly support a causal role of this founder mutation in MUSK, further expanding the gene set associated with FADS and offering new opportunities for prenatal genetic testing.

Eur J Hum Genet. 2015 Sep;23(9):1151-7.

Multiple long runs of homozygosity detected by SNP array: offspring of consanguineous parents and his siblings

Advances in Cytology & Pathology 

Long runs of homozygosity (ROHs) are frequently identified in cases interrogated by single nucleotide polymorphism (SNP) array. Presence of ROHs may be because of parental relatedness, chromosomal recombination or rearrangements and provides important clues regarding ancestral homozygosity, consanguinity or uniparental disomy. In this study we abort the use of SNP array in the detection of ROHs in an offspring of consanguineous parents and his siblings. All siblings had ROHs identified by SNP array on various chromosomes. One of them has an important ROH that harbor recessive mutation in BSDN gene. In summary, we have demonstrated that during the genetics evaluation of a patient affected by a rare disorder in the setting of consanguinity, SNP array analysis should be considered, except if the diagnosis is obvious.

Adv Cytol Pathol. 2018;3(3):56-59.

Desmosterolosis presenting with multiple congenital anomalies

European Journal of Medical Genetics

Desmosterolosis is a rare multiple congenital anomaly syndrome caused by a defect in the enzyme 3-betahydroxysterol delta-24-reductase (DHCR24) in the cholesterol biosynthesis pathway. Defects in this enzyme cause increased level of the cholesterol precursor desmosterol while disrupting development of cholesterol, impacting embryogenesis. A total of 9 cases of desmosterolosis have been reported to date. We report a 20- month-old male from consanguineous parents with multiple congenital anomalies including corpus callosum hypoplasia, facial dysmorphism, cleft palate, pectus deformity, short and wide neck and distal contractures. On analysis of the regions of homozygosity found by microarray, we identified DHCR24 as a candidate gene. Sterol quantitation showed a desmosterol level of 162 μg/mL (nl: 0.82 ± 0.48). Genetic testing confirmed the diagnosis with a homozygous likely pathogenic mutation (p.Glu191Lys) in the DHCR24 gene. Our case expands the known diagnostic spectrum for Desmosterolosis. We suggest considering Desmosterolosis in the differential diagnosis of patients who present with concurrent agenesis of the corpus callosum with white matter atrophy and ventriculomegaly, retromicrognathia with or without cleft palate, hand contractures, and delay of growth and development. Children of consanguineous mattings may be at higher risk for rare recessive disorders and testing for cholesterol synthesis defect should be a consideration for affected children. Initial evaluation can be performed using sterol quantitation, followed by genetic testing.

Eur J Med Genet. 2018 Mar;61(3):152-156.

Rare disease: a national survey of paediatricians’ experiences and needs

European Journal of Medical Genetics

Objective

To describe the experiences of Australian paediatricians while caring for children with rare diseases, and their educational and resource needs.

Design

A brief online survey was developed and deployed to a representative sample of 679 paediatricians from the Australian Paediatric Surveillance Unit database. Results Of the 679 paediatricians, 242 (36%) completed the survey. The respondents were representative of all states and territories of Australia, urban and rural regions, and hospital and private practice. Almost all respondents (93%) had seen children with one or more of >350 different rare diseases during their career; 74% had seen a new patient with rare disease in the last 6 months. The most common problems encountered while caring for patients were: diagnostic delays (65%), lack of available treatments (40%), clinical guidelines (36%) and uncertainty where to refer for peer support (35%). Few paediatricians said that rare diseases were adequately covered during university (40%) or the Fellowship of the Royal Australasian College of Physicians (50%) training, and 28% felt unprepared to care for patients with rare diseases. Paediatricians wanted lists of specialist referral services (82%) and online educational modules about rare diseases (78%) that could be accessed via one online portal that consolidated multiple resources. Smartphone applications on rare diseases were favoured by paediatricians aged <50 years and by female paediatricians.

 

Conclusions

An online educational portal should be developed and maintained for accuracy and currency of information to support dissemination of rare disease guidelines, referral pathways and coordination services relevant to Australian paediatricians and other health professionals who care for children with rare diseases.

BMJ Paediatr Open. 2017; 1(1): e000172.

Rare diseases are a ‘common’ problem for clinicians

The Royal Australian College of General practitioners

Background

Approximately 8% of the Australian population live with any one of about 10,000 known rare diseases. This is similar to the proportion of people living with diabetes or asthma.

Objectives

The aim of this article is to review the impact of rare diseases on families and health services, and the role of the general practitioner (GP) and policy response in Australia.

Discussion

Research from the Australian Paediatric Surveillance Unit indicates that people living with rare diseases face significant challenges, including diagnostic delays, lack of available treatment and difficulty in finding the right health service. Families feel isolated, under-supported, and often face economic hardship. All GPs see people with rare diseases and have a crucial role in making appropriate referrals, coordinating care, supporting families, and linking them with psychosocial and other supports. GPs require access to current, relevant resources to assist them to help patients with rare diseases. A coordinated national approach to rare diseases is also needed in Australia.

Aust Fam Physician. 2015 Sep;44(9):630-3.

Australian children living with rare diseases: experiences of diagnosis and perceived consequences of diagnostic delays

Orphanet Journal of Rare Diseases

Background

Children and families living with rare disease often experience significant health, psychosocial, economic burdens and diagnostic delays. Experiences appear to be constant, regardless of the specific rare disease diagnosis. Systematically collected Australian data to support policy response on rare diseases are scarce. We address this gap by providing survey results about 462 children aged <19 years living with approximately 200 different rare diseases.

Results

Of 462 children, 96% were born in Australia, 55% were male, median age was 8.9 years (0–18.2). Four- hundred-and-twenty-eight (93%) had received a definitive diagnosis but 29 (7%) remained undiagnosed. Before receiving the correct diagnosis 38% consulted ≥ 6 different doctors. Among those with a diagnosis, 37% believed the diagnosis was delayed and 27% initially received a wrong diagnosis. Consequences of delayed diagnosis include anxiety, loss of reproductive confidence because of an ill-defined genetic risk, frustration and stress (54%), disease progression (37%), delays in treatment (25%) and inappropriate treatments (10%). Perceived reasons for diagnostic delays included lack of knowledge about the disease among health professionals (69.2%), lack of symptom awareness by the family (21.2%) and difficulties accessing tests (17.9%). Children with inborn errors of metabolism were less likely to have a delayed diagnosis compared with other disease groups (Chi-Sq = 17.1; P < 0. 0001), most likely due to well-established and accessible biochemical screening processes. Diagnosis was given in person in 74% of cases, telephone in 18.5% and via a letter in 3.5%. Some families (16%) were dissatisfied with the way the diagnosis was delivered, citing lack of empathy and lack of information from health professionals. Psychological support at diagnosis was provided to 47.5%, but 86.2% believed that it should always be provided. Although 74.9% of parents believed that the diagnosis could have an impact on future family planning, only 44.8% received genetic counselling.

Conclusion

Parents of children living with rare chronic and complex diseases have called for better education, resourcing of health professionals to prevent avoidable diagnostic delays, and to facilitate access to early interventions and treatments. Access to psychological support and genetic counselling should be available to all parents receiving a life-changing diagnosis for their child.

Orphanet Journal of Rare Diseases. 2017 Dec;12(1):12:68.

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