Parent-of-Origin Testing for 15q11-q13 Gains by Quantitative DNA Methylation Analysis

Implementation of Nanopore sequencing as a pragmatic workflow for copy number variant confirmation in the clinic

BACKGROUND

Diagnosis of rare genetic diseases can be a long, expensive and complex process, involving an array of tests in the hope of obtaining an actionable result. Long-read sequencing platforms offer the opportunity to make definitive molecular diagnoses using a single assay capable of detecting variants, characterizing methylation patterns, resolving complex rearrangements, and assigning findings to long-range haplotypes. Here, we demonstrate the clinical utility of Nanopore long-read sequencing by validating a confirmatory test for copy number variants (CNVs) in neurodevelopmental disorders and illustrate the broader applications of this platform to assess genomic features with significant clinical implications.

METHODS

We used adaptive sampling on the Oxford Nanopore platform to sequence 25 genomic DNA samples and 5 blood samples collected from patients with known or false-positive copy number changes originally detected using short-read sequencing. Across the 30 samples (a total of 50 with replicates), we assayed 35 known unique CNVs (a total of 55 with replicates) and one false-positive CNV, ranging in size from 40 kb to 155 Mb, and assessed the presence or absence of suspected CNVs using normalized read depth.

RESULTS

Across 50 samples (including replicates) sequenced on individual MinION flow cells, we achieved an average on-target mean depth of 9.5X and an average on-target read length of 4805 bp. Using a custom read depth-based analysis, we successfully confirmed the presence of all 55 known CNVs (including replicates) and the absence of one false-positive CNV. Using the same CNV-targeted data, we compared genotypes of single nucleotide variant loci to verify that no sample mix-ups occurred between assays. For one case, we also used methylation detection and phasing to investigate the parental origin of a 15q11.2-q13 duplication with implications for clinical prognosis.

CONCLUSIONS

We present an assay that efficiently targets genomic regions to confirm clinically relevant CNVs with a concordance rate of 100%. Furthermore, we demonstrate how integration of genotype, methylation, and phasing data from the Nanopore sequencing platform can potentially simplify and shorten the diagnostic odyssey.

Complete Penetrance but Different Phenotypes in a Korean Family with Maternal Interstitial Duplication at 15q11.2-q13.1: A Case Report

The 15q duplication syndrome (dup15q) is due to the presence of at least one additional derived copy of the Prader–Willi syndrome/Angelman syndrome (PWS/AS) critical region that is approximately 5 Mb long within chromosome 15q11.2-q13.1. This report describes distinct roles of the origin of interstitial (int) dup15q underlining the critical importance of maternally active imprinted genes in the contribution to complete penetrance but different phenotypes of neuropsychotic disorders such as schizophrenia (SCZ) and autism spectrum disorder (ASD) in a Korean family. The proband’s mother as a consultant visited our hospital for her offspring’s genetic counseling and segregation analysis. She had two daughters diagnosed as SCZ or ASD and one son diagnosed as ASD. To resolve the potential genetic cause of SCZ and ASD in the proband and her sibling, whole genomic screening of chromosomal rearrangements by array-comparative genomic hybridization (CGH) was performed using SurePrint G3 Human CGH + SNP Microarray 4 × 180 K. Results of the array-CGH analysis revealed an interstitial duplication at 15q11.2-q13.1 (duplication size of 5.4 Mb) in the mother and her three offspring with SCZ or ASD. Our case, together with previous findings of high occurrence of psychotic disorder, suggest that maternally expressed gene product in the critical region of PWS/AS might mediate the risk of neurodevelopmental disorder (ASD) as well as psychotic disorder (SCZ). Multiple cytogenetic and molecular methods are recommended for investigating children with 15q11.2-q13.1 duplication and neuropsychotic disorders.

Prader-Willi Syndrome due to an Unbalanced de novo Translocation t(15;19)(q12;p13.3)

Prader-Willi syndrome (PWS) is a complex, multisystem genetic disorder characterized by endocrine, neurologic, and behavioral abnormalities. We report the first case of an unbalanced de novo reciprocal translocation of chromosomes 15 and 19, 45,XY,-15,der(19)t(15;19)(q12;p13.3), resulting in monosomy for the PWS critical chromosome region. Our patient had several typical features of PWS including infantile hypotonia, a poor suck and feeding difficulties, tantrums, skin picking, compulsions, small hands and feet, and food seeking, but not hypopigmentation, a micropenis, cryptorchidism or obesity as common findings seen in PWS at the time of examination at 6 years of age. He had seizures noted from 1 to 3 years of age and marked cognitive delay. High-resolution SNP microarray analysis identified an atypical PWS type I deletion in chromosome 15 involving the proximal breakpoint BP1. The deletion extended beyond the GABRB3 gene but was proximal to the usual distal breakpoint (BP3) within the 15q11q13 region, and GABRA5, GABRG3, and OCA2 genes were intact. No deletion of band 19p13.3 was detected; therefore, the patient was not at an increased risk of tumors from the Peutz-Jeghers syndrome associated with a deletion of the STK11 gene.

Position of the Academy of Nutrition and Dietetics: nutritional genomics

It is the position of the Academy of Nutrition and Dietetics that nutritional genomics provides insight into how diet and genotype interactions affect phenotype. The practical application of nutritional genomics for complex chronic disease is an emerging science and the use of nutrigenetic testing to provide dietary advice is not ready for routine dietetics practice. Registered dietitian nutritionists need basic competency in genetics as a foundation for understanding nutritional genomics; proficiency requires advanced knowledge and skills. Unlike single-gene defects in which a mutation in a single gene results in a specific disorder, most chronic diseases, such as cardiovascular disease, diabetes, and cancer are multigenetic and multifactorial and therefore genetic mutations are only partially predictive of disease risk. Family history, biochemical parameters, and the presence of risk factors in individuals are relevant tools for personalizing dietary interventions. Direct-to-consumer genetic testing is not closely regulated in the United States and may not be accompanied by access to health care practitioners. Applying nutritional genomics in clinical practice through the use of genetic testing requires that registered dietitian nutritionists understand, interpret, and communicate complex test results in which the actual risk of developing a disease may not be known. The practical application of nutritional genomics in dietetics practice will require an evidence-based approach to validate that personalized recommendations result in health benefits to individuals and do not cause harm.