Correction: Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach.

PURPOSE: To present results from a large cohort of individuals receiving expanded carrier screening (CS) in the United States. METHODS: Single-gene disorder carrier status for 381,014 individuals was determined using next-generation sequencing (NGS) based CS for up to 274 genes. Detection rates were compared with literature-reported values derived from disease prevalence and carrier frequencies. Combined theoretical affected pregnancy rates for the 274 screened disorders were calculated. RESULTS: For Ashkenazi Jewish (AJ) diseases, 81.6% (4434/5435) of carriers identified did not report AJ ancestry. For cystic fibrosis, 44.0% (6260/14,229) of carriers identified had a variant not on the standard genotyping panel. Individuals at risk of being a silent spinal muscular atrophy carrier, not detectable by standard screening, comprised 1/39 (8763/344,407) individuals. For fragile X syndrome, compared with standard premutation screening, AGG interruption analysis modified risk in 83.2% (1128/1356) premutation carriers. Assuming random pairing across the study population, approximately 1/175 pregnancies would be affected by a disorder in the 274-gene screening panel. CONCLUSION: Compared with standard screening, NGS-based CS provides additional information that may impact reproductive choices. Pan-ethnic CS leads to substantially increased identification of at-risk couples. These data support offering NGS-based CS to all reproductive-aged women.

Assessment of an automated approach for variant interpretation in screening for monogenic disorders: A single-center study.

BACKGROUND: Automation has been introduced into variant interpretation, but it is not known how automated variant interpretation performs on a stand-alone basis. The purpose of this study was to evaluate a fully automated computerized approach. METHOD: We reviewed all variants encountered in a set of carrier screening panels over a 1-year interval. Observed variants with high-confidence ClinVar interpretations were included in the analysis; those without high-confidence ClinVar entries were excluded. RESULTS: Discrepancy rates between automated interpretations and high-confidence ClinVar entries were analyzed. Of the variants interpreted as positive (likely pathogenic or pathogenic) based on ClinVar information, 22.6% were classified as negative (variants of uncertain significance, likely benign or benign) variants by the automated method. Of the ClinVar negative variants, 1.7% were classified as positive by the automated software. On a per-case basis, which accounts for variant frequency, 63.4% of cases with a ClinVar high-confidence positive variant were classified as negative by the automated method. CONCLUSION: While automation in genetic variant interpretation holds promise, there is still a need for manual review of the output. Additional validation of automated variant interpretation methods should be conducted.

Quality Assurance of Non-Invasive Prenatal Screening (NIPS) for Fetal Aneuploidy Using Positive Predictive Values as Outcome Measures.

Non-invasive prenatal screening (NIPS) based on the analysis of cell-free DNA in maternal plasma has been shown to have high sensitivity and specificity. We gathered follow-up information for pregnancies in women with test-positive NIPS results from 2014-2017 with quarterly assessments of positive predictive values (PPVs). A non-inferiority analysis with a minimum requirement of 70%/80% of expected performance for trisomy 21 and 18 was used to ensure testing met expectations. PPVs were evaluated in the context of changes in the population receiving testing. For all quarters, PPVs for trisomies 21 and 18 exceeded the requirement of > 70% of the reference PPV. Overall observed PPVs for trisomy 21, 18, 13 and monosomy X were similar for women aged <35 (90.9%, 95% Confidence Interval (CI) 88.6-92.7%) compared to women with advanced maternal age (94.5%, 95% CI 93.1-95.6%). Despite significant declines in test-positive rates from 1.18% to 0.62% for trisomy 21, and from 0.75% to 0.48% for trisomies 18, 13 and monosomy X combined, PPVs remained stable through the four-year interval. We conclude that quarterly evaluation of PPV provides an overview of past testing and helps demonstrate long-term consistency in test performance, even in the setting of increasing use by women with lower a priori risks.

Cytogenetic biomarkers for human cancer.

Human cancer cytogenetics is the study of chromosomal rearrangements and numerical abnormalities in malignant tissue. Since the 1960s and the discovery of the Philadelphia chromosome, hundreds of common and characteristic chromosomal aberrations have been observed in various neoplasias. Because these cytogenetic aberrations provide diagnostic, prognostic, and treatment-related information for the associated cancers, they are considered biomarkers for disease. Here we describe many of the best-known chromosome rearrangements and variant rearrangements in hematologic disease and solid tumors, indicate the genes and underlying molecular mechanisms known to be involved in development and progression of disease, and describe the newer molecular cytogenetic technologies and how they are currently being used in cancer diagnostics. We also highlight many important pit-falls in obtaining, transporting, and analyzing neoplastic samples which can compromise cytogenetic studies and preclude its use as a diagnostic tool.

Genetics and epidemiology of Tourette syndrome.

Although the genetic basis of Tourette syndrome is well established, uncertainty about how best to define and assess the Tourette syndrome phenotype has hampered efforts to identify the genes responsible for susceptibility to the disorder. In addition, such efforts have typically been underpowered or were undertaken before the technology was available to perform systematic genome-wide genetic investigations. The Tourette Syndrome Association International Consortium on Genetics was formed by more than a dozen research groups from around the world to develop common approaches to phenotyping Tourette syndrome and to pool samples for uniform, well-powered genetic investigations. Several recent advances, including the completion of genome-wide scans of affected sib-pairs and large families, show real promise for identifying Tourette syndrome susceptibility genes. In this review, we describe the key epidemiologic, linkage, and association studies in Tourette syndrome and illustrate the strategies currently being used to identify Tourette syndrome genes.

Validation and clinical application of a locus-specific polymerase chain reaction- and minisequencing-based assay for congenital adrenal hyperplasia (21-hydroxylase deficiency).

Congenital adrenal hyperplasia is an autosomal recessive disorder caused by defective adrenal steroid biosynthesis, resulting in reduced glucocorticoid and increased androgen production. The majority of cases are due to inactivation of the 21-hydroxylase gene (CYP21A2), most commonly caused by genomic rearrangements with the adjacent, highly homologous pseudogene CYP21A. The most common deletions and gene conversion events have been defined and are typically detected by Southern hybridization detection of CYP21 rearrangements and/or polymerase chain reaction (PCR). However, Southern hybridization is laborious, and allele-specific PCR results may be difficult to interpret. We have therefore developed a locus-specific, PCR-based, minisequencing method for detecting the 12 most common CYP21A2 mutations. We validated the assay using a panel of 20 previously genotyped samples obtained from individuals who collectively have a broad spectrum of mutations causing 21-hydroxylase deficiency. We also used 19 control samples having no CYP21 mutations. All validation samples were correctly typed, and we identified haplotypes that may be useful for clinical diagnosis. Results from 102 clinical samples demonstrate that this assay is a rapid, reliable, and robust method for locus-specific identification of mutations and is suitable for routine clinical use and prenatal diagnosis.

Microelectronic array system for molecular diagnostic genotyping: Nanogen NanoChip 400 and molecular biology workstation.

Hundreds of gene mutations responsible for Mendelian disorders are currently tested in the clinical laboratory for pre- and postnatal diagnosis, carrier screening and presymptomatic testing. Since human genetic research is currently focused on determining the etiology of complex diseases, including heart disease, diabetes and neuropsychiatric traits, laboratorians will genotype increasing numbers of clinically relevant loci in the future. This will require accurate, high-throughput and cost-effective genotyping platforms, such as the DNA microarray. The Nanogen NanoChip platforms employ hybridization-based technology, using fluorescent detection and electronic control of the target or probe, to obtain clear genotype signal relative to background, and increased flexibility relative to similar chip-based single nucleotide polymorphism genotyping platforms. The scope of this review is intended to describe the operating principle, chips and instrumentation, analyte-specific reagents, published assay protocols, assay development, and clinical use of the NanoChip platforms. It is beyond the scope of this review to describe the use of NanoChip platforms in basic research, and to compare it against all available clinical single nucleotide polymorphism genotyping applications and platforms.

Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses.

Rare sequence variants may be important in understanding the biology of common diseases, but clearly establishing their association with disease is often difficult. Association studies of such variants are becoming increasingly common as large-scale sequence analysis of candidate genes has become feasible. A recent report suggested SLITRK1 (Slit and Trk-like 1) as a candidate gene for Tourette Syndrome (TS). The statistical evidence for this suggestion came from association analyses of a rare 3'-UTR variant, var321, which was observed in two patients but not observed in more than 2000 controls. We genotyped 307 Costa Rican and 515 Ashkenazi individuals (TS probands and their parents) and observed var321 in five independent Ashkenazi parents, two of whom did not transmit this variant to their affected child. Furthermore, we identified var321 in one subject from an Ashkenazi control sample. Our findings do not support the previously reported association and suggest that var321 is overrepresented among Ashkenazi Jews compared with other populations of European origin. The results further suggest that overrepresentation of rare variants in a specific ethnic group may complicate the interpretation of association analyses of such variants, highlighting the particular importance of precisely matching case and control populations for association analyses of rare variants.