scholarly journals Uniparental disomy in a population of 32,067 clinical exome trios

2021 ◽  
Author(s):  
Julie Scuffins ◽  
Jennifer Keller-Ramey ◽  
Lindsay Dyer ◽  
Ganka Douglas ◽  
Rebecca Torene ◽  
...  
Keyword(s):  
Copy Number ◽  
Diagnostic Testing ◽  
Uniparental Disomy ◽  
Copy Number Variant ◽  
Diagnostic Value ◽  
Chromosomal Microarray ◽  
Pathogenic Variants ◽  
Imprinting Disorder ◽  
Disease Associations ◽  
Diagnostic Finding

Abstract Purpose Data on the clinical prevalence and spectrum of uniparental disomy (UPD) remain limited. Trio exome sequencing (ES) presents a comprehensive method for detection of UPD alongside sequence and copy-number variant analysis. Methods We analyzed 32,067 ES trios referred for diagnostic testing to create a profile of UPD events and their disease associations. ES single-nucleotide polymorphism (SNP) and copy-number data were used to identify both whole-chromosome and segmental UPD and to categorize whole-chromosome results as isodisomy, heterodisomy, or mixed. Results Ninety-nine whole-chromosome and 13 segmental UPD events were identified. Of these, 29 were associated with an imprinting disorder, and 16 were associated with a positive test result through homozygous sequence variants. Isodisomy was more commonly observed in large chromosomes along with a higher rate of homozygous pathogenic variants, while heterodisomy was more frequent in chromosomes associated with imprinting or trisomy mosaicism (14, 15, 16, 20, 22). Conclusion Whole-chromosome UPD was observed in 0.31% of cases, resulting in a diagnostic finding in 0.14%. Only three UPD-positive cases had a diagnostic finding unrelated to the UPD. Thirteen UPD events were identified in cases with prior normal SNP chromosomal microarray results, demonstrating the additional diagnostic value of UPD detection by trio ES.

scholarly journals Copy number variants in clinical WGS: deployment and interpretation for rare and undiagnosed disease

2018 ◽  
Author(s):  
Andrew M Gross ◽  
Subramanian S. Ajay ◽  
Vani Rajan ◽  
Carolyn Brown ◽  
Krista Bluske ◽  
...  
Keyword(s):  
Copy Number ◽  
De Novo ◽  
Genetic Disorders ◽  
Diagnostic Testing ◽  
Copy Number Variants ◽  
Uniparental Disomy ◽  
Copy Number Variant ◽  
Break Point ◽  
Clinically Significant ◽  
Family Based

AbstractPurposeCurrent diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, whole genome sequencing (WGS) has the potential to detect all genomic mutation types on a single platform and workflow. Here we sought to evaluate copy number variant (CNV) calling as part of a clinically accredited WGS test.MethodsUsing a depth-based copy number caller we performed analytical validation of CNV calling on a reference panel of 17 samples, compared the sensitivity of WGS-based variants to those from a clinical microarray, and set a bound on precision using orthogonal technologies. We developed a protocol for family-based analysis, annotation, filtering, visualization of WGS based CNV calls, and deployed this across a clinical cohort of 79 rare and undiagnosed cases.ResultsWe found that CNV calls from WGS are at least as sensitive as those from microarrays, while only creating a modest increase in the number of variants interpreted (~10 CNVs per case). We identified clinically significant CNVs in 15% of the first 79 cases analyzed. This pipeline also enabled identification of cases of uniparental disomy (UPD) and a 50% mosaic trisomy 14. Directed analysis of some CNVs enabled break-point level resolution of genomic rearrangements and phasing of de-novo CNVs.ConclusionRobust identification of CNVs by WGS is possible within a clinical testing environment, and further developments will bring improvements in resolution of smaller and more complex CNVs.

Utility of SNP Microarray in the Diagnosis of MDS

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4806-4806
Author(s):  
Peter Papenhausen ◽  
Stuart Schwartz ◽  
Henry Y. Dong ◽  
Alan F. List ◽  
Ronald Thomason
Keyword(s):  
Copy Number ◽  
Neutral Loss ◽  
Diagnostic Testing ◽  
Uniparental Disomy ◽  
Selective Advantage ◽  
Copy Number Alterations ◽  
Driver Genes ◽  
Jak2 Mutation ◽  
Snp Microarray ◽  
Early Primary

Abstract Abstract 4806 A series of 206 bone marrow aspirates/blood submitted for diagnostic testing for possible MDS/MPN was studied by high resolution SNP microarray to determine the efficacy of this technology for detecting clonal copy number alterations and copy neutral loss of heterozygosity. The latter, acquired uniparental disomy (aUPD), is associated with oncogene mutations that through mitotic recombination have converted to the homozygous state, offering additional selective advantage to daughter cells. Of the 206 patient samples classified as possible MDS, 76 were abnormal by the array. Thirty one of these were either copy neutral or demonstrated copy number alterations below the resolution of cytogenetics. Twenty-three cases demonstrated aUPD and in 14 of these it was the only abnormality detected. Two of these 14 had multiple aUPD (9q/14q and 1p/4q/14q). When the aUPD clones were accompanied by copy number alterations, they could be seen as either the early primary alteration or as a later evolutionary event. The most common segmental UPD regions in MDS were 4q(9), 7q(4),11q(4) and 14q(4) while 9p(4) was the most common a(UPD in the patients with MPN which was likely to be associated with a homozygous JAK2 mutation (confirmed in two cases). The small MPN group (12 cases) demonstrated eight clones with aUPD, only three of which had copy number alterations. All the aUPDs found in this study involved terminal chromosome arm exchange and almost all involved a percentage of the DNA tested, consistent with an acquired change. Whole chromosome aUPD was not seen in these patients. There were three instances of possible interstitial LOH which were not included in this report until normal patient DNA can be obtained to confirm this uncommon observation. Two of these three showed mosaic LOH consistent with an acquired change. The most common deletions below the resolution of cytogenetics involved the RUNX1 and TET2 genes. In summary, the SNP microarray increased the abnormal clone detection from 45 by cytogenetics to 76 in cases of MDS and from 4 to 8 in the small MPN cohort, underscoring the utility of the testing while laying the groundwork for the discovery of new driver genes in the aUPD regions in the pathogenesis of MDS. Disclosures: Papenhausen: LabCorp: Employment. Schwartz:LabCorp: Employment. Thomason:LabCorp: Employment.

scholarly journals JAX-CNV: A whole genome sequencing-based algorithm for copy number detection at clinical grade level

2021 ◽  
Author(s):  
Wan-Ping Lee ◽  
Qihui Zhu ◽  
Xiaofei Yang ◽  
Silvia Liu ◽  
Eliza Cerveira ◽  
...  
Keyword(s):  
False Discovery Rate ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variant ◽  
Fold Increase ◽  
Chromosomal Microarray ◽  
Whole Genome ◽  
False Discovery ◽  
Calling Algorithm

We aimed to develop a whole genome sequencing (WGS)-based copy number variant (CNV) calling algorithm with the potential of replacing chromosomal microarray assay (CMA) for clinical diagnosis. JAX-CNV is thus developed for CNV detection from WGS. The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the results of clinically-validated CMAs. Comparing to 112 CNVs reported by clinically-validated CMAs of the 31 samples, JAX-CNV is 100% recalling them. Besides, JAX-CNV identified an average of 30 CNVs per individual that is an approximately seven-fold increase compared to calls of clinically-validated CMAs. Experimental validation of 24 randomly selected CNVs, showed one false positive (i.e., a false discovery rate of 4.17%). A robustness test on lower-coverage data revealed a 100% sensitivity for CNVs greater than 300 kb (the current threshold for College of American Pathologists) down to 10x coverage. For CNVs greater than 50 kb, sensitivities were 100% for coverages deeper than 20x, 97% for 15x, and 95% for 10x. We developed a WGS-based CNV pipeline, including this newly developed CNV caller JAX-CNV, and found it capable of detecting CMA reported CNVs at 100% sensitivity with about 4% false discovery rate. We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS. JAX-CNV is available on https://github.com/TheJacksonLaboratory/JAX-CNV.

scholarly journals Genetics and Clinical Features of Noncompaction Cardiomyopathy in the Fetal Population

2021 ◽  
Vol 7 ◽  
Author(s):  
Hairui Sun ◽  
Xiaoyan Hao ◽  
Xin Wang ◽  
Xiaoxue Zhou ◽  
Ye Zhang ◽  
...  
Keyword(s):  
Congenital Heart Defects ◽  
Copy Number ◽  
Congenital Heart ◽  
Heart Defects ◽  
Gene Mutations ◽  
Copy Number Variant ◽  
Sequencing Analysis ◽  
Noncompaction Cardiomyopathy ◽  
Pathogenic Variants ◽  
Clinical Awareness

Objectives: Noncompaction Cardiomyopathy (NCCM) has been classified as primary genetic cardiomyopathy and has gained increasing clinical awareness; however, little is known about NCCM in the fetal population. We aimed to investigate the clinical characteristics and genetic spectrum of a fetal population with NCCM.Methods: We retrospectively reviewed all fetuses with a prenatal diagnosis of NCCM at a single center between October 2010 and December 2019. These cases were investigated for gestational age at diagnosis, gender, left or biventricular involvement, associated cardiac phenotypes, outcomes, and genetic testing data.Results: We identified 37 fetuses with NCCM out of 49,898 fetuses, indicating that the incidence of NCCM in the fetal population was 0.07%. Of the 37 fetuses, 26 were male, ten were female and one was of unknown gender. NCCM involvement biventricle is the most common (n = 16, 43%), followed by confined to the left ventricle (n = 14, 38%). Nineteen (51%) had additional congenital heart defects, with right-sided lesions being the most common (n = 14, 74%), followed by ventricular septal defects (n = 10, 53%). Hydrops fetalis was present in 12 cases (32%), of which four were atypical (pericardial effusion only). Sequencing analysis was performed at autopsy (n = 19) or postnatally (n = 1) on 20 fetuses. Of the 20 fetuses undergoing copy number variation sequencing and whole-exome sequencing, nine (47%) had positive genetic results, including one with a pathogenic copy number variant and eight with pathogenic/likely pathogenic variants. Non-sarcomere gene mutations accounted for the vast majority (n = 7). In contrast, sarcomere gene mutations occurred in only one case (TPM1), and no mutations were identified in the three most common sarcomere genes (MYH7, TTN, and MYBPC3) of pediatric and adult patients. Pathogenic/likely pathogenic variants were significantly more frequent in fetuses with congenital heart defects than those without congenital heart defects.Conclusions: Our data demonstrate that fetal NCCM is a unique entity. Compared with pediatric and adult NCCM, fetal NCCM is more prone to biventricle involvement, more likely to be complicated with congenital heart defects, and has a distinct genetic spectrum.

Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays

2015 ◽  
Vol 146 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Weiqiang Liu ◽  
Rui Zhang ◽  
Jun Wei ◽  
Huimin Zhang ◽  
Guojiu Yu ◽  
...  
Keyword(s):  
Copy Number ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Copy Number Variations ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Imprinting Disorders ◽  
Genome Wide ◽  
Number Variation ◽  
Efficient Alternative

Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD.

scholarly journals Peruvian Newborn Male with 3p13 Deletion Syndrome Encompassing the FOXP1 Gene: Review of the Literature

2020 ◽  
Vol 09 (04) ◽  
pp. 270-278
Author(s):  
Hugo H. Abarca-Barriga ◽  
Milana Trubnykova ◽  
Félix Chavesta-Velásquez ◽  
Claudia Barletta-Carrillo ◽  
Marco Ordoñez-Linares ◽  
...  
Keyword(s):  
Copy Number ◽  
Choanal Atresia ◽  
Copy Number Variant ◽  
Autism Spectrum ◽  
Deletion Syndrome ◽  
Chromosomal Microarray ◽  
Facial Dysmorphism ◽  
Chromosomal Microarray Analysis ◽  
Heart Malformation ◽  
Number Variation

AbstractCopy number variation in loss of 3p13 is an infrequently reported entity characterized by hypertelorism, aniridia, microphthalmia, high palate, neurosensorial deafness, camptodactyly, heart malformation, development delay, autism spectrum disorder, seizures, and choanal atresia. The entity is caused probably by haploinsufficiency for FOXP1, UBA3, FAM19A1, and MITF. We report a newborn male with hypotonia, facial dysmorphism, heart malformation, and without clinical diagnosis; nevertheless, the use of appropriate genetic test, such us the chromosomal microarray analysis allowed identification of a copy number variant in loss of 5.5 Mb at chromosome 3 (p13-p14.1), that included 54 genes, encompassing FOXP1 gene. We compare the findings in our Peruvian patient to those of earlier reported patients; furthermore, add new signs for this entity.

scholarly journals Exome sequencing as a first-tier test for copy number variant detection : retrospective evaluation and prospective screening in 2418 cases.

2021 ◽  
Author(s):  
Quentin TESTARD ◽  
Xavier VANHOYE ◽  
Laure RAYMOND ◽  
Jean-Francois TALY ◽  
Marie-Emmanuelle NAUD-BARREYRE ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Copy Number ◽  
Diagnostic Yield ◽  
Incidental Finding ◽  
Copy Number Variant ◽  
Chronic Kidney Failure ◽  
Copy Number Variations ◽  
Chromosomal Microarray ◽  
Diagnostic Work ◽  
Work Up

Purpose: Despite exome (ES) or genome sequencing (GS) availability, chromosomal microarray (CMA) remains the first-line diagnostic tests in most rare disorders diagnostic work-up, looking for Copy-number variations (CNV), with a diagnostic yield of 10-20%. The question of the equivalence of CMA and ES in CNV calling is an organisational and economic question, especially when ordering a GS after a negative CMA and/or ES. Methods: This work measures the equivalence between CMA and GATK4 exome sequencing depth of coverage method in detecting coding CNV on a retrospective cohort of 615 unrelated individuals. A prospective detection of ES CNV on a cohort of 1803 unrelated individuals was performed. Results: On the retrospective validation cohort every CNV was accurately detected (64/64 events). In the prospective cohort, 32 diagnostics were performed among the 1803 individuals with CNVs ranging from 704bp to aneuploidy. An incidental finding was reported. The overall increase in diagnostic yield was of 1.7%, varying from 1.2% in individuals with multiple congenital anomalies to 1.9% in individuals with chronic kidney failure. Conclusions: Combining SNV and CNV detection increases the suitability of exome sequencing as a first-tier diagnostic test for suspected rare mendelian disorders. Before considering the prescription of a GS after a negatif ES, a careful reanalysis with updated CNV calling and SNV annotation should be considered.

Osteogenesis Imperfecta and Split Foot Malformation due to 7q21.2q21.3 Deletion Including COL1A2, DLX5/6 Genes: Review of the Literature

2021 ◽  
Author(s):  
Özden Öztürk ◽  
Haydar Bagis ◽  
Semih Bolu
Keyword(s):  
Osteogenesis Imperfecta ◽  
Copy Number ◽  
Bone Fractures ◽  
Genetic Disorder ◽  
Rare Condition ◽  
Copy Number Variant ◽  
Joint Laxity ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Number Variation

AbstractCopy number variation in loss of 7q21 is a genetic disorder characterized by split hand/foot malformation, hearing loss, developmental delay, myoclonus, dystonia, joint laxity, and psychiatric disorders. Osteogenesis imperfecta caused by whole gene deletions of COL1A2 is a very rare condition. We report a Turkish girl with ectrodactyly, joint laxity, multiple bone fractures, blue sclera, early teeth decay, mild learning disability, and depression. A copy number variant in loss of 4.8 Mb at chromosome 7 (q21.2q21.3) included the 58 genes including DLX5, DLX6, DYNC1I1, SLC25A13, SGCE, and COL1A2. They were identified by chromosomal microarray analysis. We compared the findings in our patients with those previously reported. This case report highlights the importance of using microarray to identify the genetic etiology in patients with ectrodactyly and osteogenesis imperfecta.

scholarly journals MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6183 ◽  
Author(s):  
Pavlina Capkova ◽  
Josef Srovnal ◽  
Zuzana Capkova ◽  
Katerina Staffova ◽  
Vera Becvarova ◽  
...  
Keyword(s):  
Clinical Significance ◽  
Diagnostic Testing ◽  
Copy Number Variants ◽  
Ring Chromosome ◽  
Autism Spectrum ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Rare Cnvs ◽  
Pathogenic Variants ◽  
Dependent Probe

Background Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. Method We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. Result Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)—likely pathogenic, 10 VOUS—uncertain, and 58 VOUS—likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS—likely pathogenic, and six designated as VOUS—likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS—likely pathogenic, or VOUS—uncertain in multiple patients. Moreover, the studied ASD cohort exhibited significant (p < 0.05) enrichment of duplications encompassing DOCK8. Conclusion Multiplex ligation-dependent probe amplification and CMA yielded concordant results for 12 patients bearing CNV designated pathogenic or VOUS—likely pathogenic. Unambiguous diagnoses were achieved for eight patients (corresponding to 8.7% of the total studied population) by both MLPA and CMA, for one (1.09%) patient by karyotyping, and for one (1.09%) patient by FRAXA testing. MLPA and CMA thus achieved identical reliability with respect to clinically relevant findings. As such, MLPA could be useful as a fast and inexpensive test in patients with syndromic autism. The detection rate of potentially pathogenic variants (VOUS—likely pathogenic) achieved by CMA was higher than that for MLPA (13.04% vs. 4.35%). However, there was no corresponding difference in the rate of unambiguous diagnoses of ASD patients. In addition, the results obtained suggest that DOCK8 may play a role in the etiology of ASD.

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