Biomedical subjects

Martin J Somerville

Publications and source records attributed to Martin J Somerville.

10 recordsLinked to original sources

PubMed2025

Comparing the performance of exome and genome sequencing for rare disease diagnostics: A randomized implementation effectiveness trial.

PURPOSE: Exome sequencing (ES) and genome sequencing (GS) can improve rare disease diagnosis but are not routinely available in many jurisdictions. To inform implementation, we report on a randomized implementation effectiveness trial comparing ES and GS. METHODS: Eligible trios were randomized to receive ES or GS in the same clinically accredited laboratory. Patient-level data on diagnostic utility and turnaround times were collected. Outcomes were compared statistically between clinically important subgroups. RESULTS: Of 1048 patients, 68.5% had syndromic intellectual disability/developmental delay (ID/DD) and 20.5% had multisystem disorders without ID/DD. Most had prior genetic test(s) that were nondiagnostic (95.5%), and of these, 91.6% included chromosome microarray. Diagnostic yields were 33.8% and 33.6%, for ES (n = 526) and GS (n = 522), respectively. Within sequencing groups, diagnostic results were more frequent among those with ID/DD than those without (P < .005). For routine (ie, nonexpedited) patients (n = 1020), 87.0% were reported in <12 weeks, and the mean turnaround time was 55.5 days (SD: 24.0). Turnaround time for ES and GS did not differ; however, result type (P < .001) and age of onset (P < .005) significantly affected turnaround time. CONCLUSION: Findings provide robust evidence of diagnostic utility and timeliness of ES and GS and will inform policy related to the organization, delivery, and reimbursement of clinical-grade genome diagnostics for rare diseases.

Adolescent↗

PubMed2025

A microcosting and cost consequence analysis from a randomized controlled trial comparing genome sequencing with exome sequencing for genetic diagnosis.

PURPOSE: Diagnosing rare diseases is costly. The objectives were to microcost exome (ES) and genome sequencing (GS) trios and estimate the incremental costs of GS per additional diagnosis from an institutional payer perspective. METHODS: Trios (proband plus biological parents) that are referred for sequencing were randomly assigned to ES or GS. Laboratory workflow and sequencing were microcosted. Total and category cost per trio were estimated probabilistically. Effectiveness was expressed as diagnostic yield (rates of diagnostic or partially diagnostic variants detected). Incremental costs and effectiveness were calculated. RESULTS: The mean total cost per trio was CAD 2888.79 (95% CI 2567.72, 3492.72) for ES (n = 329) and 4364.02 (95% CI 3984.94, 5013.67) for GS (n = 324). Reagents accounted for 34% and 61% of total costs for ES and GS, respectively. The incremental cost of GS was 1475.23. The diagnostic yield was 35.9% for ES and 32.7% for GS with a difference of 0.032 (95% CI: -0.041, 0.104, P value .397). CONCLUSION: GS demonstrated higher costs and a similar diagnostic yield to ES but was limited by technical capabilities at the time of the study. The study provides comprehensive costs for the economic evaluation comparing alternative diagnostic pathways and impetus for further evaluating variants uniquely detectable by GS.

Humans↗

PubMed2006

Global variation in copy number in the human genome.

Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.

Chromosome Mapping↗

PubMed2005

Severe expressive-language delay related to duplication of the Williams-Beuren locus.

The Williams-Beuren syndrome (WBS) locus, at 7q11.23, is prone to recurrent chromosomal rearrangements, including the microdeletion that causes WBS, a multisystem condition with characteristic cardiovascular, cognitive, and behavioral features. It is hypothesized that reciprocal duplications of the WBS interval should also occur, and here we present such a case description. The most striking phenotype was a severe delay in expressive speech, in contrast to the normal articulation and fluent expressive language observed in persons with WBS. Our results suggest that specific genes at 7q11.23 are exquisitely sensitive to dosage alterations that can influence human language and visuospatial capabilities.

Attention Deficit Disorder with Hyperactivity↗

PubMed2005

Mapping of a single locus capable of complementing the defective heterochromatin phenotype of Roberts syndrome cells.

Roberts syndrome (RS) is a developmental disorder characterized by tetraphocomelia and a broad spectrum of additional clinical features. Most patients with RS exhibit characteristic cytogenetic phenotypes, which include an abnormal appearance of pericentromeric heterochromatin on metaphase chromosomes, referred to as "heterochromatic repulsion." In the present study, we use complementation of this abnormal cytogenetic phenotype as a means to identify a specific region of the normal human genome capable of rendering phenotypic correction. We screened the entire human genome, using a transient chromosome-transfer assay, and demonstrated complementation exclusively after the transfer of proximal chromosome 8p, a result subsequently confirmed by stable microcell-mediated chromosome transfer. Additionally, homozygosity mapping was used to refine the interval of this complementing locus to 8p21. The results are consistent with the notion that the single gene defect responsible for heterochromatic splaying and developmental abnormalities maps to chromosome 8p21.

Abnormalities, Multiple↗

PubMed2005

Microduplication and triplication of 22q11.2: a highly variable syndrome.

22q11.2 microduplications of a 3-Mb region surrounded by low-copy repeats should be, theoretically, as frequent as the deletions of this region; however, few microduplications have been reported. We show that the phenotype of these patients with microduplications is extremely diverse, ranging from normal to behavioral abnormalities to multiple defects, only some of which are reminiscent of the 22q11.2 deletion syndrome. This diversity will make ascertainment difficult and will necessitate a rapid-screening method. We demonstrate the utility of four different screening methods. Although all the screening techniques give unique information, the efficiency of real-time polymerase chain reaction allowed the discovery of two 22q11.2 microduplications in a series of 275 females who tested negative for fragile X syndrome, thus widening the phenotypic diversity. Ascertainment of the fragile X-negative cohort was twice that of the cohort screened for the 22q11.2 deletion. We also report the first patient with a 22q11.2 triplication and show that this patient's mother carries a 22q11.2 microduplication. We strongly recommend that other family members of patients with 22q11.2 microduplications also be tested, since we found several phenotypically normal parents who were carriers of the chromosomal abnormality.

Abnormalities, Multiple↗

PubMed2004

Chromosome 1q21.1 contiguous gene deletion is associated with congenital heart disease.

Congenital heart disease (CHD), comprising structural or functional abnormalities present at birth, is the most common birth defect in humans. Reduced expression of connexin40 (Cx40) has been found in association with atrial fibrillation, and deletion of Cx40 in a mouse model causes various structural heart abnormalities in 18% of heterozygotes. We screened 505 unrelated CHD cases for deletions or duplications of the Cx40 gene (GJA5) by real-time quantitative PCR, in order to determine whether altered copy number of this gene may be associated with a cardiac phenotype in humans. Dosage of Cx40 flanking genes (ACPL1 and Cx50 gene, GJA8) was determined by real-time PCR for all apparent positive cases. In total, 3 cases were found to carry deletions on chromosome 1q21.1 spanning ACPL1, Cx40, and Cx50 genes. Absence of heterozygosity was observed in all 3 index cases over a 1.5- to 3-Mb region. Samples from the parents of two cases were obtained, and microsatellites across 1q21.1 were genotyped. One of the apparently unaffected parents was found to carry this deletion. All 3 index cases presented with obstruction of the aortic arch as the common structural cardiac malformation, and had no consistent dysmorphic features. Genotyping of 520 unrelated normal controls for this deletion was negative. We hypothesize that this 1q21.1 multigene deletion is associated with a range of cardiac defects, with anomalies of the aortic arch being a particular feature.

Acid Phosphatase↗

PubMed2003

Integration of combined heteroduplex/restriction fragment length polymorphism analysis on an electrophoresis microchip for the detection of hereditary haemochromatosis.

This work describes an integrated method of enzymatic digestion, heteroduplex analysis (HA) and electrophoretic sizing on a microfluidic chip. HA techniques based on microchip electrophoresis are capable of the high sensitivity detection of subtle mutations such as single nucleotide polymorphisms (SNPs) but are not readily able to detect homozygous mutant genotypes. Such homozygous conditions are commonly encountered with the gene implicated in hereditary haemochromatosis, HFE. We employed the restriction fragment length polymorphism (RFLP) method of mutation detection to complement the HA method in a rapid novel on-chip procedure that separated digested PCR fragments to reliably determine the presence or absence of the most important mutations associated with haemochromatosis. This method was able to distinguish the homozygous mutant, heterozygous and homozygous wildtype genotypes. The mutations investigated here (C282Y, H63D and S65C) are often the mutation targets used in the genetic testing for haemochromatosis. This method provides the extremely specific digestion methods needed for the analysis of the known and relatively common mutations that have a significant probability of occurring in a homozygous form. However, the high sensitivity of the HA method is useful in detecting other mutations of lesser likelihood which, by virtue of their rarity, are likely to be present only in a heterozygous form. Although the conventional methods of analysing these mutations require as much as a day to perform, this microchip method, even without robotics or multiplexed operation, can be performed in about 10 min per sample.

Electrophoresis↗

PubMed2003

Heteroduplex-based genotyping with microchip electrophoresis and dHPLC.

This work compares the methods of mutation detection via denaturing high-performance liquid chromatography (dHPLC) and a microchip-based heteroduplex analysis (HA) method. The mutations analyzed were 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2 with, as additional examples, 188del11 and 5396 + 1G --> A in BRCA1. Our HA method is based upon the use of a replaceable, highly denaturing sieving matrix that has dynamic coating capabilities, rendering our method relatively insensitive to contamination. We have found significant advantages in the microchip analysis in terms of reagent consumption, ease of use, versatility, simplicity of the protocol, the lack of constraints upon sample preparation or content, and the lack of parameters that need be adjusted. Although HA methods have a lower sensitivity than that of dHPLC, the electropherograms of the present HA method appear to provide more information and may allow mutations within the same amplicon to be distinguished. Although the dHPLC method has a remarkably high sensitivity, with this sensitivity there come constraints that may prevent it, in its present form, from being used in some applications, particularly those involving higher levels of integration. The advantages of the present HA method, along with recent developments in microchip-based single-nucleotide polymorphism (SNP) detection and high-throughput arrays, suggest that microchip-based systems could provide compact and integrated platforms capable of large-scale genotyping or mutational screening.

BRCA1 Protein↗

PubMed2002

A homozygous germ-line mutation in the human MSH2 gene predisposes to hematological malignancy and multiple café-au-lait spots.

Individuals with a germ-line mutation in one of the DNA mismatch repair (MMR) genes are at significant risk for colorectal cancer and other tumors. Three families have previously been reported with individuals homozygous for mutations in the MMR gene MLH1 that are predicted to compromise MMR. These individuals develop hematological malignancies and/or neurofibromatosis type 1 at an early age. Here, in an individual, we demonstrate that a homozygous novel mutation in the MMR gene MSH2 is associated with leukemia and multiple café-au-lait spots, a feature of neurofibromatosis type 1. Because the hematological malignancies observed in the individuals homozygous for the loss of MMR are reflective of the lymphomas seen in mice lacking MMR, the mice may provide a useful model for human neoplasia.

Adaptor Proteins, Signal Transducing↗