The Journal of Molecular Diagnostics

BackgroundLarge scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. ResultsSJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate...

BackgroundThe RCCX locus, resulting from segmental duplication, exhibits extensive sequence identity and modular variations because of unequal crossover events, leading to copy number variations and the formation of chimeric genes between active and pseudogenes. Precise characterization of this locus is essential for molecular diagnosis, because aberrations within this region can cause congenital adrenal hyperplasia (CAH), an autosomal recessive disorder. However, the intricate modular structure...

Optical genome mapping (OGM) is an emerging technology with great potential for prenatal diagnosis. OGM can identify and resolve all types of balanced and unbalanced cytogenomic abnormalities in a single test, which are typically assessed by multiple standard of care (SOC) methods including karyotyping, fluorescence in situ hybridization and chromosomal microarray. To assess OGMs viability as an alternative to conventional SOC testing, a comprehensive clinical research study was conducted acros...

Accurate diagnosis and risk stratification of hematological malignancies require disease-specific laboratory testing procedures involving the use of hematopathology, flow cytometry, molecular, and cytogenetic testing. While individual laboratories develop unique workflows to accommodate volume, clinical needs, and staffing, cytogenetic laboratories generally require a multitude of targeted and genome-wide tests that detect clinically relevant aberrations in hematologic malignancies. Specifically...

ImportanceHereditary hematopoietic malignancies (HHMs) are hereditary cancer syndromes that constitute at least 14% of all myeloid malignancies, but genetic assays used to diagnose HHMs have historically been of variable quality. Here, we demonstrate that HHM assays continue to have persistent shortcomings. These diagnostic gaps place patients with HHMs at high risk for missed diagnoses, missed opportunities for cancer screening, and donor-derived leukemias following stem cell transplant. Objec...

An implementation of the windows based DLBCL automatic classification (DAC) algorithm for determining cell of origin (COO) written in the R language and designed for use with the HTG EdgeSeq Reveal Software package is described. Classifications using the new implementation (DAC-R) were compared to the those using the original version (DAC-Win), the HTG DLBCL COO classifier, the HTG EdgeSeq Reveal DLBCL algorithm. Classifications made using HTG data were tested for concordance with those made usi...

BackgroundLiquid biopsy (LBx) assays are transforming precision oncology by the screening of genomic alterations in cfDNA. These assays provide a less invasive alternative to tissue biopsies, which are not always feasible. Molecular pathology laboratories require LBx assays that detect variants at low allele frequencies using standardized methods. MethodsThis study evaluated the Hedera Profiling 2 ctDNA test panel (HP2) (Hedera Dx, Epalinges, Switzerland), a hybrid capture-based NGS assay for t...

Genetic diseases encompass a spectrum of disorders resulting from DNA variations. Preimplantation genetic testing (PGT) is a critical strategy for preventing recurrent miscarriage, foetal malformations, and the birth of children affected by chromosomal abnormalities and monogenic disorders. Traditional PGT techniques necessitate comprehensive pedigree genetic data for haplotype linkage analysis, whereas PGT employing third-generation sequencing (TGS) has distinct advantages, particularly in case...

Molecular Tumour Boards (MTBs) rely on different bioinformatics tools and knowledgebases for variant annotation, oncogenicity classification, and estimation of complex biomarkers to identify actionable alterations. However, the typical bioinformatics workflow to process raw next-generation sequencing (NGS) data into clinically meaningful variants involves multiple steps and is inherently complex, thus requiring repeated manual intervention and causing delays in providing molecularly informed pre...

Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), employed globally for the past three decades have significant limitations in the resolution or the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS) based technologies are now widely used to detect clinically significant sequence variants b...

Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers a computationally-driven target enrichment technology, adaptive sampling, which enables intensive analysis of...

PurposeClinical analysis and reporting of somatically acquired copy number abnormalities (CNAs) detected through next-generation sequencing (NGS) is time consuming and requires significant expertise. Interpretation is complicated by other classes of variants such as coding mutations and gene fusions. Recent guidelines for the clinical assessment of tumor CNAs harmonize and simplify the reporting criteria but did not directly address NGS-specific concerns or the need for a standardized and scalab...

ObjectivesTo investigate the incidence of chromosomal abnormalities in the products of conception (POC) of patients with spontaneous miscarriages (SM) and with recurrent pregnancy losses (RPL), and to determine biological mechanisms contributing to RPL. DesignRetrospective cohort study. SettingUniversity-affiliated medical center. PatientsDuring a 20-years period, 12,096 POC samples underwent classical chromosome analysis as a part of standard clinical care. InterventionsCytogenetic findings...

BACKGROUNDCirculating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing, but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separators, which are routinely used in clinical chemistry, as an accessible and underutilized source for cfDNA biobanking and testing. METHODSWe analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing tube comparison acr...

PurposeWe previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive preimplantation genetic testing (PGT) solution. Haploseek is based on microarray genotyping of the embryos parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek. MethodsWe developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo bas...

BackgroundIdentification and confirmation of copy number variation is an important aspect of genetic testing for several prenatal scenarios, such as abnormal maternal serum screening, abnormal ultrasound findings, high risk results on non-invasive prenatal screening as well as postnatal settings such as developmental delay, intellectual disabilities, congenital anomalies and dysmorphism as well as in couples with recurrent miscarriages. Low pass whole genome sequencing (lpWGS) followed by copy n...

Clinical checklists are the current gold standard to determine whether a child with cancer shows indications for genetic testing. Nevertheless, the efficacy of these tests to reliably detect genetic cancer predisposition in children with cancer is still insufficiently investigated. Here, we assessed the validity of clinically recognizable signs to identify cancer predisposition by correlating a state-of-the-art clinical checklist to the corresponding whole exome sequencing analysis in an unselec...

Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate...

Despite advances in cancer therapeutics, early detection is often the best prognostic indicator for survival (1). People with Li-Fraumeni syndrome harbor a germline pathogenic variant in the tumor suppressor gene TP53 (2) and face a near 100% lifetime risk of developing a wide spectrum of, often multiple, cancers (3). TP53 mutation carriers routinely undergo intensive surveillance protocols which, although associated with significantly improved survival, are burdensome to both the patient and th...

ObjectiveThis study evaluates the diagnostic utility of low-pass whole genome sequencing (LP-WGS) for the detection of chromosomal abnormalities in Amniotic fluid samples (AFS), Chorionic villi samples (CVS) and Product of conception (POC) samples from India. MethodsA total of 1508 prenatal samples including - AFS, CVS and POC were analyzed using LP-WGS at either low-resolution ([~]0.5-1X) or high-resolution ([~]5X). CNV analysis was performed using StrandNGS v4.2 and Variant Intelligence Appli...