Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing

BACKGROUND

Despite clinically demonstrated accuracy in next generation sequencing (NGS) data, many clinical laboratories continue to confirm variants with Sanger sequencing, which increases cost of testing and turnaround time. Several studies have assessed the accuracy of NGS in detecting single nucleotide variants; however, less has been reported about insertion, deletion, and deletion-insertion variants (indels).

METHODS

We performed a retrospective analysis from 2015-2022 of indel results from a subset of NGS targeted gene panel tests offered through the Mayo Clinic Genomics Laboratories. We compared results from NGS and Sanger sequencing of indels observed in clinical runs and during the intra-assay validation of the tests.

RESULTS

Results demonstrated 100% concordance between NGS and Sanger sequencing for over 490 indels (217 unique), ranging in size from 1 to 68 basepairs (bp). The majority of indels were deletions (77%) and 1 to 5 bp in length (90%). Variant frequencies ranged from 11.4% to 67.4% and 85.1% to 100% for heterozygous and homozygous variants, respectively, with a median depth of coverage of 2562×. A subset of indels (7%) were located in complex regions of the genome, and these were accurately detected by NGS. We also demonstrated 100% reproducibility of indel detection (n = 179) during intra-assay validation.

CONCLUSIONS

Together this data demonstrates that reportable indel variants up to 68 bp can be accurately assessed using NGS, even when they occur in complex regions. Depending on the complexity of the region or variant, Sanger sequence confirmation of indels is usually not necessary if the variants meet appropriate coverage and allele frequency thresholds.

Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach

CYP2D6 duplication has important pharmacogenomic implications. Reflex testing with long-range PCR (LR-PCR) can resolve the genotype when a duplication and alleles with differing activity scores are detected. We evaluated whether visual inspection of plots from real-time-PCR-based targeted genotyping with copy number variation (CNV) detection could reliably determine the duplicated CYP2D6 allele. Six reviewers evaluated QuantStudio OpenArray CYP2D6 genotyping results and the TaqMan Genotyper plots for seventy-three well-characterized cases with three copies of CYP2D6 and two different alleles. Reviewers blinded to the final genotype visually assessed the plots to determine the duplicated allele or opt for reflex sequencing. Reviewers achieved 100% accuracy for cases with three CYP2D6 copies that they opted to report. Reviewers did not request reflex sequencing in 49-67 (67-92%) cases (and correctly identified the duplicated allele in each case); all remaining cases (6-24) were marked by at least one reviewer for reflex sequencing. In most cases with three copies of CYP2D6, the duplicated allele can be determined using a combination of targeted genotyping using real-time PCR with CNV detection without need for reflex sequencing. In ambiguous cases and those with >3 copies, LR-PCR and Sanger sequencing may still be necessary for determination of the duplicated allele.

Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

PURPOSE

The Mayo-Baylor RIGHT 10K Study enabled preemptive, sequence-based pharmacogenomics (PGx)-driven drug prescribing practices in routine clinical care within a large cohort. We also generated the tools and resources necessary for clinical PGx implementation and identified challenges that need to be overcome. Furthermore, we measured the frequency of both common genetic variation for which clinical guidelines already exist and rare variation that could be detected by DNA sequencing, rather than genotyping.

METHODS

Targeted oligonucleotide-capture sequencing of 77 pharmacogenes was performed using DNA from 10,077 consented Mayo Clinic Biobank volunteers. The resulting predicted drug response-related phenotypes for 13 genes, including CYP2D6 and HLA, affecting 21 drug-gene pairs, were deposited preemptively in the Mayo electronic health record.

RESULTS

For the 13 pharmacogenes of interest, the genomes of 79% of participants carried clinically actionable variants in 3 or more genes, and DNA sequencing identified an average of 3.3 additional conservatively predicted deleterious variants that would not have been evident using genotyping.

CONCLUSION

Implementation of preemptive rather than reactive and sequence-based rather than genotype-based PGx prescribing revealed nearly universal patient applicability and required integrated institution-wide resources to fully realize individualized drug therapy and to show more efficient use of health care resources.

Targeted Genotyping in Clinical Pharmacogenomics: What Is Missing?

Clinical pharmacogenomic testing typically uses targeted genotyping, which only detects variants included in the test design and may vary among laboratories. To evaluate the potential patient impact of genotyping compared with sequencing, which can detect common and rare variants, an in silico targeted genotyping panel was developed based on the variants most commonly included in clinical tests and applied to a cohort of 10,030 participants who underwent sequencing for CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, CYP3A5, DPYD, SLCO1B1, TPMT, UGT1A1, and VKORC1. The results of in silico targeted genotyping were compared with the clinically reported sequencing results. Of the 10,030 participants, 2780 (28%) had at least one potentially clinically relevant variant/allele identified by sequencing that would not have been detected in a standard targeted genotyping panel. The genes with the largest number of participants with variants only detected by sequencing were SLCO1B1, DPYD, and CYP2D6, which affected 13%, 6.3%, and 3.5% of participants, respectively. DPYD (112 variants) and CYP2D6 (103 variants) had the largest number of unique variants detected only by sequencing. Although targeted genotyping detects most clinically significant pharmacogenomic variants, sequencing-based approaches are necessary to detect rare variants that collectively affect many patients. However, efforts to establish pharmacogenomic variant classification systems and nomenclature to accommodate rare variants will be required to adopt sequencing-based pharmacogenomics.

392Systematic review and meta-analysis on the diagnostic accuracy for the detection of relevant coronary artery stenosis of vasodilator myocardial perfusion CMR and dobutamine stress echocardiography

Background

Relevance of coronary artery stenosis in patients with stabile coronary artery disease (SCAD) is defined by myocardial ischemia due to flow limitation. While FFR-guided treatment of SCAD is a class IA recommendation. The initial risk stratification with detection of relevant CAD can be facilitated by several myocardial imaging methods without any preference mentioned in current guidelines.

Objectives

This study aimed to systematically assess and to compare the diagnostic accuracy of vasodilator myocardial perfusion cardiovascular magnetic resonance imaging (pCMR) and dobutamine stress echocardiography (DSE) for the non-invasive detection of relevant SCAD through a meta-analysis, to enable an evidential preference in risk stratification. In contrast to previously published work, this meta-analysis explicitly included only studies with rigorous eligibility criteria and a narrowly prespecified definition of their invasive reference tests.

Selection criteria

A study was included if (1) CCA or FFR was used as a reference standard for diagnosing relevant SCAD, defined as >70% stenosis or a value <0.80 on FFR recordings, respectively; (2) sufficient data to permit analysis and to reconstruct contingency tables (explicitly true-positive, false-positive, false-negative and true-negative findings) was provided; (3) there was a minimal sample size of 20 patients; (4) assessment of myocardial perfusion reserve was performed using vasodilators adenosine or regadenoson for pCMR, and dobutamine used for echocardiography; and (5) the studies were of prospective design.

Data collection and analysis: From the 5,634 studies identified, 1,306 relevant articles were selected after title screening. Just 47 fulfilled all inclusion criteria on full-text review, resulting in a total sample size of 4,742 patients. Data extraction was performed for each study by two reviewers independently.Pooled analysis was performed based on a random effects models.

Results

The sensitivity, specificity and diagnostic odds ratio (DOR) for pCMR were 0.88 (95% confidence interval (CI): 0.85–0.90), 0.84 (95% CI: 0.81–0.87), and 38 (95% CI: 29–49), and for DSE 0.72 (95% CI: 0.61–0.81), 0.89 (95% CI: 0.83–0.93), and 20 (95% CI: 9–46), respectively. Post-test probability was augmented by positive (likelihood ratio) LR of 5.5 (95% CI: 4.7–6.5) and negative LR of 0.14 (95% CI: 0.12–0.18) based on Bayes' theorem, as compared to LR of 6.3 (95% CI: 3.8, 10.4) and negative LR of 0.31 (95% CI: 0.21, 0.46) for DSE. The size of the prediction region on the hierarchical summary receiver operating characteristic (HSROC) plot for pCMR (0.29; 95% CI 0.11–0.77) was significantly smaller compared to the one of DSE (1.07; 95% CI 0.27–4.19; p<0.01).

Forrest plot pCMR

Conclusion

The results of this systematic review and meta-analysis show that pCMR is characterized by a superior diagnostic test accuracy of relevant SCAD compared to DSE and that it can refine the post-test probability of SCAD.

Acknowledgement/Funding

European Heart Academy of the European Society of Cardiology

Genetic variation in statin intolerance and a possible protective role for UGT1A1

The etiology of statin intolerance is hypothesized to be due to genetic variants that impact statin disposition and clearance. We sought to determine whether genetic variants were associated to statin intolerance. The studied cohort consisted of hyperlipidemic participants (n = 90) clinically diagnosed with statin intolerance by a cardiologist and matched controls without statin intolerance. Creatine kinase activity, lipid profiles and genetic analyses were performed on genes involved in statin metabolism and included UGT1A1 and UGT1A3 sequencing and targeted analyses of CYP3A4*22, CYP3A5*3, SLCO1B1*5 and *1b, ABCB1 c.3435C>T, ABCG2 c.421C>A and GATM rs9806699. Although lipids were higher in cases, genetic variant minor allele frequencies were similar between cases and controls, except for UGT1A1*28, which was less prevalent in cases than controls.

Preemptive Pharmacogenomic Testing for Precision Medicine: A Comprehensive Analysis of Five Actionable Pharmacogenomic Genes Using Next-Generation DNA Sequencing and a Customized CYP2D6 Genotyping Cascade

Significant barriers, such as lack of professional guidelines, specialized training for interpretation of pharmacogenomics (PGx) data, and insufficient evidence to support clinical utility, prevent preemptive PGx testing from being widely clinically implemented. The current study, as a pilot project for the Right Drug, Right Dose, Right Time-Using Genomic Data to Individualize Treatment Protocol, was designed to evaluate the impact of preemptive PGx and to optimize the workflow in the clinic setting. We used an 84-gene next-generation sequencing panel that included SLCO1B1, CYP2C19, CYP2C9, and VKORC1 together with a custom-designed CYP2D6 testing cascade to genotype the 1013 subjects in laboratories approved by the Clinical Laboratory Improvement Act. Actionable PGx variants were placed in patient's electronic medical records where integrated clinical decision support rules alert providers when a relevant medication is ordered. The fraction of this cohort carrying actionable PGx variant(s) in individual genes ranged from 30% (SLCO1B1) to 79% (CYP2D6). When considering all five genes together, 99% of the subjects carried an actionable PGx variant(s) in at least one gene. Our study provides evidence in favor of preemptive PGx testing by identifying the risk of a variant being present in the population we studied.

Prospective assessment of fetal-maternal cell transfer in miscarriage and pregnancy termination

BACKGROUND

Fetal cells (microchimerism) are acquired by women during pregnancy. Fetal microchimerism persists decades later and includes cells with pluripotent capacity. Persistent microchimerism has the capacity for both beneficial and detrimental maternal health consequences. Both miscarriage and termination of pregnancy can result in fetal microchimerism. We sought to determine whether cellular fetal microchimerism is acquired during management of pregnancy loss and further explored factors that could influence fetal cell transfer, including viability of fetal tissue, surgical versus medical management and gestational age.

METHODS

Pregnant women (n= 150 samples from 75 women) with singleton pregnancies undergoing a TOP (n= 63) or treatment for embryonic or fetal demise (miscarriage, n= 12) were enrolled. Mononuclear cells were isolated from blood samples drawn before, and 30 min after, treatment. Fetal cellular microchimerism concentrations were determined using quantitative PCR for a Y chromosome-specific sequence, expressed as genome equivalents of fetal DNA per 100 000 maternal cell equivalents (gEq/10(5)). Detection rate ratios were determined according to clinical characteristics.

RESULTS

Cellular fetal microchimerism was found more often in post- compared with pretreatment samples, 24 versus 5% (P= 0.004) and at higher concentrations, 0-36 versus 0-0.7 gEq/10(5) (P< 0.001). Likelihood of microchimerism was higher in surgical than medical management, detection rate ratio 24.7 (P= 0.02). The detection rate ratio for TOP versus miscarriage was 16.7 for known male fetuses (P= 0.02). Microchimerism did not vary with gestational age.

CONCLUSIONS

Significant fetal cell transfer occurs during miscarriage and TOP. Exploratory analyses support relationships between obstetric clinical factors and acquisition of fetal cellular microchimerism; however, our limited sample size precludes definitive analysis of these relationships, and confirmation is needed. In addition, the long-term persistence and potential consequences of fetal microchimerism on maternal health merit further investigation.

CYP2D6*11 and challenges in clinical genotyping of the highly polymorphic CYP2D6 gene

CYP2D6 is genotyped clinically for prediction of response to tamoxifen, psychotropic drugs and other medications. Phenotype prediction is dependent upon accurate genotyping. The CYP Allele Nomenclature Committee maintains the allelic nomenclature for CYP2D6; however, in some cases, the list of polymorphisms associated with a given allele is incomplete. Clinical laboratories and in vitro diagnostic manufacturers rely upon this nomenclature, in addition to the literature, to infer allelic function and haplotypes and when they design CYP2D6-testing platforms. This article provides more complete sequencing data for the CYP2D6*11 allele and describes the difficulties encountered in genotyping CYP2D6 when incomplete data are available. The CYP Allele Nomenclature Committee should provide clear information about the completeness of the original data used to define each allele.

Aneuploidy in the normal and diseased brain

The brain is remarkable for its complex organization and functions, which have been historically assumed to arise from cells with identical genomes. However, recent studies have shown that the brain is in fact a complex genetic mosaic of aneuploid and euploid cells. The precise function of neural aneuploidy and mosaicism are currently being examined on multiple fronts that include contributions to cellular diversity, cellular signaling and diseases of the central nervous system (CNS). Constitutive aneuploidy in genetic diseases has proven roles in brain dysfunction, as observed in Down syndrome (trisomy 21) and mosaic variegated aneuploidy. The existence of aneuploid cells within normal individuals raises the possibility that these cells might have distinct functions in the normal and diseased brain, the latter contributing to sporadic CNS disorders including cancer. Here we review what is known about neural aneuploidy, and offer speculations on its role in diseases of the brain.

The function of a stem-loop in telomerase RNA is linked to the DNA repair protein Ku

The telomerase enzyme lengthens telomeres, an activity essential for chromosome stability in most eukaryotes. The enzyme is composed of a specialized reverse transcriptase and a template RNA. In Saccharomyces cerevisiae, overexpression of TLC1, the telomerase RNA gene, disrupts telomeric structure. The result is both shortened telomere length and loss of a special chromatin structure that normally silences telomere-proximal genes. Because telomerase function is not required for telomeric silencing, we postulated that the dominant-negative effect caused by overexpression of TLC1 RNA originates in a normal interaction between the RNA and an unknown telomeric factor important for silencing; the overexpressed RNA presumably continues to bind the factor and compromises its function. Here we show that a 48-nt stem-loop structure within the 1.3-kb TLC1 RNA is necessary and sufficient for disrupting telomeric silencing and shortening telomeres. Moreover, this short RNA sequence appears to function through an interaction with the conserved DNA end-binding protein Ku. We propose that, in addition to its roles in telomeric silencing, homologous recombination and non-homologous end-joining (NHEJ), S. cerevisiae Ku also helps to recruit or activate telomerase at the telomere through an interaction with this stem-loop of TLC1 RNA.

Hürthle cell adenoma diagnosed by core needle biopsy in a male patient

Hürthle cell adenomas (HCAs) are a rare and potentially lethal variant of follicular tumors of the thyroid. Considerable controversy exists regarding potential risk factors, diagnosis, and treatment of HCAs. The authors report the case of a 38-year-old male patient with an 8.3 cm x 3.5 cm HCA. Diagnosis was made preoperatively from a core needle biopsy and confirmed postoperatively on frozen section. Treatment consisted of a right lobectomy.

Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae

The ends of chromosomes in Saccharomyces cerevisiae initiate a repressive chromatin structure that spreads internally and inhibits the transcription of nearby genes, a phenomenon termed telomeric silencing. To investigate the molecular basis of this process, we carried out a genetic screen to identify genes whose overexpression disrupts telomeric silencing. We thus isolated 10 DOT genes (disruptor of telomeric silencing). Among these were genes encoding chromatin component Sir4p, DNA helicase Dna2p, ribosomal protein L32, and two proteins of unknown function, Asf1p and Ifh1p. The collection also included genes that had not previously been identified: DOT1, DOT4, DOT5, DOT6, and TLC1, which encodes the RNA template component of telomerase. With the exception of TLC1, all these genes, particularly DOT1 and DOT4, also reduced silencing at other repressed loci (HM loci and rDNA) when overexpressed. Moreover, deletion of the latter two genes weakened silencing as well, suggesting that DOT1 and DOT4 normally play important roles in gene repression. DOT1 deletion also affected telomere tract length. The function of Dot1p is not known. The sequence of Dot4p suggests that it is a ubiquitin-processing protease. Taken together, the DOT genes include both components and regulators of silent chromatin.

Management of blood-drawing fears in adolescents with comorbid anxiety and depressive disorders

As more pharmacologic treatment and research on child and adolescent psychiatric patients are conducted, the common problem of blood-drawing fears will need to be addressed. Avoidance of blood-drawing could jeopardize an individual's physical and mental health, and inhibit the collection of data aimed at furthering the study of psychiatric disorders in youth. This report describes the naturalistic application of specific techniques for managing severe blood-drawing fears in adolescent subjects undergoing a clinical trial. The adolescents (ages 12-18) were 44 consecutive school refusers with comorbid anxiety and major depressive disorders. Of the school-refusing adolescents, 27% (12 of 44) were observed to have a severe fear of blood-drawing. A management strategy comprised of providing information, distraction, supportive reassurance, and exposure appeared successful in managing the fears of blood-drawing in all of the adolescents, except two. These 2 adolescents refused to enter the treatment study due to a marked fear of blood-drawing. All 10 subjects who exhibited a fear of blood-drawing and were able to complete the initial blood test, using the interventions noted, were able to obtain subsequent venipunctures with minimal or no avoidance behavior. These preliminary findings suggest that blood-drawing fears can be effectively managed in most cases, though controlled studies of these interventions are needed.

Muscular strength and bone density with weight training in middle-aged women

Previous research has demonstrated positive correlations between bone mass and both physical activity and muscular strength. There is a paucity of information describing the specific type of exercise which most benefits the human skeleton. The effects of a 1 yr weight training program on 18 middle-aged women participating in an endurance dance program (E + W) compared with 17 other women in the endurance dance program only (E) and with 19 sedentary controls (C) were studied by measuring muscular strength and bone mineral density (BMD). Eighteen women in the E + W group demonstrated increases in all strength measurements, whereas the E and C groups either had smaller increases or had declined. A significant group x test interaction term, indicating that groups responded differently over time, was observed for nondominant isokinetic elbow flexion measured through the range of motion at a constant velocity of 60 degrees.s-1 (P less than 0.05), nondominant isokinetic elbow extension at 180 degrees.s-1 (P less than 0.01), and nondominant isokinetic elbow flexion at 180 degrees.s-1 (P less than 0.05). BMD did not change significantly except that a significant group x test interaction term appeared for the radius ultradistal site (P less than 0.01). BMD of the humerus and femoral Ward's triangle increased nonsignificantly in both E and E + W over the year. This weight training program increased muscular strength but did not increase measured bone mass.

Prudent laboratory usage, cost containment, and high quality medical care: are they compatible?

Inappropriate laboratory use by physicians is partly responsible for the rapid rise in health care costs. This use falls into three categories--over-, under-, and misutilization. Overuse creates information overload for the physician and has a detrimental effect on patient care. Abnormal results are frequently obscured by massive amounts of requested information. Studies show that laboratory use is greater for younger physicians and that increased use is not associated with better outcome of care. Overuse ranges from 26 per cent to 98 per cent for selected tests. Unnecessary tests can be eliminated with no adverse effect on quality. Laboratory use can be improved by a variety of approaches including education, feedback, implementation of administrative changes and, finally, financial incentives or disincentives; the last has proven the most effective. All the approaches should be reinforced by cost-conscious clinical settings that foster a "why" rather than a "why not" philosophy. Improving laboratory use may reduce costs and maintain quality.

GMENAC report on U.S. physician manpower policies: recommendations and reactions

After four years of study in the United States, the Graduate Medical Education National Advisory Committee (GMENAC) concluded that an excess of approximately 70,000 physicians will exist in 1990. Faced with a future surplus, GMENAC recommends that U.S. medical schools decrease enrollment levels by 10 percent relative to the 1978-79 level and severely restrict entrance of foreign medical graduates. Flaws identified in the GMENAC approach relate to the use of the delphi technique, the future role of nonphysician providers, and a lack of reliable data. The GMENAC report may provide impetus for an abrupt shift from expansionism to reductionism in U.S. physician manpower policy. Long range physician manpower planning has erred in the past, necessitating periodic reevaluation of national policy. A continuing balance between supply and demand, although ideal, can probably never be attained. Thus small adjustments in total supply and specialty mix will always be necessary. The GMENAC report, which is the most comprehensive study of U.S. physician manpower to date, requires serious consideration in this context.

Evaluation and validation of a course in practice management for senior residents

Many doctors reach the end of their specialist training to find that they need to cope well and efficiently with the business aspects of setting up and managing a medical practice-yet this has frequently been ignored in their education. This article describes the design and evaluation of a course in practice management offered to doctors near the end of their specialist training.

Community-based Practitioners as Medical Student Preceptors-Dispelling an Old Myth

This study was designed to compare the teaching abilities of community-based preceptors and university-based clinical faculty, as judged by two matched groups of students. On only one of 13 dimensions of clinical teaching was there a significant difference between the preceptors and university-based faculty: preceptors were reported to use demonstrations less than their university-based colleagues. The study shows that despite their other commitments and lack of formal training in didactic skills, community-based practitioners can provide sound educational experiences and, in the students' opinions, are as competent teachers as clinical, university-based faculty.

A calcified fibrocartilagenous nodule in the ligamentum nuchae. Presenting as a tumor

Nodules of fibrocartilage, calcified fibrocartilage, or bone may be found in the adult ligamentum nuchae. These are generally asymptomatic but may mimic fractures or, as in the case presented here, tumors.