Genomic sequencing in clinical practice: applications, challenges, and opportunities

The impact of supplementing traditional risk information with polygenic risk score concerning type 2 diabetes and coronary heart disease on health behavior: a randomized controlled trial

Polygenic risk scores (PRS) for different diseases are expected to become more widely available to the public in the coming decades. In addition to the investigation of the clinical relevance of polygenic risk scores, an assessment of the health behavioral impact is needed. The present study used data from a personalized medicine project that combined genomic and traditional health data to evaluate respondents' risk for common diseases. Specifically, we investigated if supplementing traditional risk estimates of type 2 diabetes and coronary heart disease with PRS influenced respondents' self-reported physical activity, alcohol consumption, fruit/vegetable consumption or prompted the respondents to seek medical treatment/examination. As an exploratory hypothesis, we also tested if there was an interaction between the disease risk level and the experimental/control group for any of the outcomes. A randomized controlled trial was conducted, where the experimental group (n = 216 for seeking treatment and 523-459 for other outcomes) received risk estimates based on traditional risk and PRS, and the control group (n = 216 and 526-498) based solely on traditional risk factors. On average, approximately 80 days elapsed between the risk disclosure and outcome measurements. We found no significant difference between the groups regarding health behavior (ps > .28, ds < 0.07) or likelihood of seeking medical treatment/examination (p = .86, OR = 1.06). Likewise, no significant interactions were detected (ps > .08, ds < .11, ORs < 1.2). We conclude that we did not find support for either a beneficial or detrimental effect of supplementing traditional risk estimates with PRSs. However, several limitations should be noted when generalizing the results.

SNPscan Combined With CNVplex as a High-Performance Diagnostic Method for Thalassemia

OBJECTIVE

Thalassemia is a Mendelian-inherited blood disorder with severe consequences, including disability and mortality, making it a significant public health concern. Therefore, there is an urgent need for precise diagnostic technologies. We introduce two innovative diagnostic techniques for thalassemia, SNPscan and CNVplex, designed to enhance molecular diagnostics of thalassemia.

METHODS

The SNPscan and CNVplex assays utilize variations in PCR product length and fluorescence to identify multiple mutations. In the SNPscan method, we designed three probes per locus: two 5' and one 3', and incorporated allele identification link sequences into one of the 5' probes to distinguish the alleles. The detection system was designed for 67 previously reported loci in the Chinese population for a specific genetic condition. CNVplex identifies deletion types by analyzing the specific positions of probes within the globin gene. This innovative approach enables the detection of six distinct deletional mutations, enhancing the precision of thalassemia diagnostics. We evaluated and refined the methodologies in a training cohort of 100 individuals with confirmed HBA and HBB genotypes. The validation cohort, consisting of 1647 thalassemia patients and 100 healthy controls, underwent a double-blind study. Traditional diagnostic techniques served as the control methods.

RESULTS

In the training set of 100 samples, 10 mutations (Hb QS, Hb CS, Hb Westmead, CD17, CD26, CD41-42, IVS-II-654, --SEA, -α3.7 and -α4.2) were identified, consistent with those identified by traditional methods. The validation study showed that SNPscan/CNVplex offered superior molecular diagnostic capabilities for thalassemia, with 100% accuracy compared to 99.43% for traditional methods. Notably, the assay identified three previously undetected mutations in 10 cases, including two deletion mutations (Chinese Gγ(Aγδβ)0 del and SEA-HPFH), and one non-deletion mutation (Hb Q-Thailand).

CONCLUSIONS

The SNPscan/CNVplex assay is a cost-effective and user-friendly tool for diagnosing thalassemia, demonstrating high accuracy and reliability, and showing great potential as a primary diagnostic method in clinical practice.

Research participants' perspectives about the return of uninformative genomic test results in a clinical research setting

The majority of genomic sequencing and microarray results are clinically uninformative, meaning that they do not suggest a need for any behavioral action or medical intervention. Prior studies have shown that recipients of uninformative genomic testing results ("uninformative results" hereafter) may incorrectly interpret them to imply a lowered risk of disease or false reassurance about future health risks. Few studies have examined how patients understand uninformative results when they are returned in a research setting, where there is wide variation in analytical specifications of testing, interpretation and reporting practices, and resources to support the return of results. We conducted cross-sectional interviews (N = 17) to explore how a subset of research participants in one genomics study at the National Institutes of Health reacted to and understood their uninformative test results, which were returned to them via a patient portal without genetic counseling. We found that most participants did not remember the details of the informed consent process, including the distinction between "primary" and "secondary" findings. Participants had questions about what genes were tested for and, in most cases, requested a list of the genes covered. Several participants incorrectly assumed that autosomal recessive carrier results would have been reported to them if detected. Some participants interpreted their uninformative results to mean that they could forgo prenatal testing, and participants had mixed expectations about whether their results might be reinterpreted in the future. These themes suggest that there are specific challenges to returning uninformative results in research settings. Educational supplements to uninformative test reports may be most useful if they contextualize results in relation to other types of clinical genetic or genomic testing that may be made available to research participants in their lifetimes.

Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning

MOTIVATION

Whole-exome and genome sequencing have become common tools in diagnosing patients with rare diseases. Despite their success, this approach leaves many patients undiagnosed. A common argument is that more disease variants still await discovery, or the novelty of disease phenotypes results from a combination of variants in multiple disease-related genes. Interpreting the phenotypic consequences of genomic variants relies on information about gene functions, gene expression, physiology, and other genomic features. Phenotype-based methods to identify variants involved in genetic diseases combine molecular features with prior knowledge about the phenotypic consequences of altering gene functions. While phenotype-based methods have been successfully applied to prioritizing variants, such methods are based on known gene-disease or gene-phenotype associations as training data and are applicable to genes that have phenotypes associated, thereby limiting their scope. In addition, phenotypes are not assigned uniformly by different clinicians, and phenotype-based methods need to account for this variability.

RESULTS

We developed an Embedding-based Phenotype Variant Predictor (EmbedPVP), a computational method to prioritize variants involved in genetic diseases by combining genomic information and clinical phenotypes. EmbedPVP leverages a large amount of background knowledge from human and model organisms about molecular mechanisms through which abnormal phenotypes may arise. Specifically, EmbedPVP incorporates phenotypes linked to genes, functions of gene products, and the anatomical site of gene expression, and systematically relates them to their phenotypic effects through neuro-symbolic, knowledge-enhanced machine learning. We demonstrate EmbedPVP's efficacy on a large set of synthetic genomes and genomes matched with clinical information.

AVAILABILITY AND IMPLEMENTATION

EmbedPVP and all evaluation experiments are freely available at https://github.com/bio-ontology-research-group/EmbedPVP.

Access and barriers to genomic classifiers for breast cancer and prostate cancer in India

The incidence of cancer in general, including breast and prostate cancer specifically, is increasing in India. Breast and prostate cancers have genomic classifiers developed to guide therapy decisions. However, these genomic classifiers are often inaccessible in India due to high cost. These classifiers may also be less suitable to the Indian population, as data primarily from patients in wealthy Western countries were used in developing these genomic classifiers. In addition to the limitations in using these existing genomic classifiers, developing and validating new genomic classifiers for breast and prostate cancer in India is challenging due to the heterogeneity in the Indian population. However, there are steps that can be taken to address the various barriers that currently exist for accurate, accessible genomic classifiers for cancer in India.

Potential Drug-Nutrient Interactions of 45 Vitamins, Minerals, Trace Elements, and Associated Dietary Compounds with Acetylsalicylic Acid and Warfarin-A Review of the Literature

In cardiology, acetylsalicylic acid (ASA) and warfarin are among the most commonly used prophylactic therapies against thromboembolic events. Drug-drug interactions are generally well-known. Less known are the drug-nutrient interactions (DNIs), impeding drug absorption and altering micronutritional status. ASA and warfarin might influence the micronutritional status of patients through different mechanisms such as binding or modification of binding properties of ligands, absorption, transport, cellular use or concentration, or excretion. Our article reviews the drug-nutrient interactions that alter micronutritional status. Some of these mechanisms could be investigated with the aim to potentiate the drug effects. DNIs are seen occasionally in ASA and warfarin and could be managed through simple strategies such as risk stratification of DNIs on an individual patient basis; micronutritional status assessment as part of the medical history; extensive use of the drug-interaction probability scale to reference little-known interactions, and application of a personal, predictive, and preventive medical model using omics.

Multilevel barriers and facilitators to widespread use of preconception carrier screening in the United States

PURPOSE

Although preconception reproductive genetic carrier screening (RGCS) is preferred to screening during pregnancy, population-wide preconception screening is not routinely performed in the United States. We explored the multilevel barriers to the widespread adoption of preconception RGCS in the United States via key informant interviews.

METHODS

Semi-structured virtual video interviews were conducted with 29 informants with a breadth of professional expertise between May and October 2022. Data collection and qualitative analyses were guided by the Consolidated Framework for Implementation Research and socioecological model. Analysis focused on identifying barriers to delivering preconception RGCS at and across different levels of health care and exploring potential facilitators of preconception RGCS delivery.

RESULTS

Barriers to preconception RGCS were identified at the levels of test characteristics, patients and couples, clinicians and care teams, and the external health care and policy environments. Across the different levels of care delivery, 3 themes of barriers emerged: (1) fragmentation and inconsistencies hinder care delivery, (2) gaps in knowledge, misconceptions, and uncertainties about RGCS are pervasive, and (3) expanding preconception RGCS in the diverse US population presents unique implementation challenges. Potential solutions were detailed by informants.

CONCLUSION

Identifying individual and thematic barriers to preconception RGCS delivery may help to define strategies to alleviate obstacles.

From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus

Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.

Proteomics-Driven Biomarkers in Pancreatic Cancer

Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.

Utilization of multiple genetic methods for prenatal diagnosis of rare thalassemia variants

Background: Thalassemia is the most prevalent monogenic disorder caused by an imbalance between the α- and β-globin chains as a result of pathogenic variants in the α- or β-globin genes. Novel or complex structural changes in globin genes are major hurdles for genetic consulting and prenatal diagnosis. Methods: From 2020 to 2022, genetic analysis was performed on 1,316 families suspected of having children with thalassemia major, including 42 pregnant couples suspected of being thalassemia carriers with rare variants. Multiple techniques including multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, targeted next-generation sequencing, and single-molecule real-time (SMRT) sequencing were used to diagnose rare thalassemia. Results: The rate of prenatal diagnosis for rare thalassemia variants was 3.19% (42/1,316). The most prevalent alleles of α- and β-thalassemia are Chinese ^Gγ(^Aγδβ)⁰and -- ^THAI deletion. In addition, ten rare complex genotypes include one Chinese ^Gγ(^Aγδβ)⁰ deletion combined with HBG1-HBG2 fusion, two rare deletions at HBB gene (hg38, Chr11: 5224211-5232470, hg38, Chr11: 5224303-5227790), one complete 7,412 bp fusion gene for anti-Lepore Hong Kong, two complex rearrangements of the α-globin gene cluster, two novel duplications, and two rare large deletions in the α-globin gene cluster. Conclusion: Accurate gene diagnosis for probands with combined molecular biology techniques is the key to prenatal diagnosis of rare thalassemia.

Biomarkers for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): a systematic review

BACKGROUND

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multifaceted condition that affects most body systems. There is currently no known diagnostic biomarker; instead, diagnosis is dependent on application of symptom-based case criteria following exclusion of any other potential medical conditions. While there are some studies that report potential biomarkers for ME/CFS, their efficacy has not been validated. The aim of this systematic review is to collate and appraise literature pertaining to a potential biomarker(s) which may effectively differentiate ME/CFS patients from healthy controls.

METHODS

This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Cochrane review guidelines. PubMed, Embase and Scopus were systematically searched for articles containing "biomarker" and "ME/CFS" keywords in the abstract or title and if they included the following criteria: (1) were observational studies published between December 1994 and April 2022; (2) involved adult human participants; (3) full text is available in English (4) original research; (5) diagnosis of ME/CFS patients made according to the Fukuda criteria (1994), Canadian Consensus Criteria (2003), International Consensus Criteria (2011) or Institute of Medicine Criteria (2015); (6) study investigated potential biomarkers of ME/CFS compared to healthy controls. Quality and Bias were assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Case Control Studies.

RESULTS

A total of 101 publications were included in this systematic review. Potential biomarkers ranged from genetic/epigenetic (19.8%), immunological (29.7%), metabolomics/mitochondrial/microbiome (14.85%), endovascular/circulatory (17.82%), neurological (7.92%), ion channel (8.91%) and physical dysfunction biomarkers (8.91%). Most of the potential biomarkers reported were blood-based (79.2%). Use of lymphocytes as a model to investigate ME/CFS pathology was prominent among immune-based biomarkers. Most biomarkers had secondary (43.56%) or tertiary (54.47%) selectivity, which is the ability for the biomarker to identify a disease-causing agent, and a moderate (59.40%) to complex (39.60%) ease-of-detection, including the requirement of specialised equipment.

CONCLUSIONS

All potential ME/CFS biomarkers differed in efficiency, quality, and translatability as a diagnostic marker. Reproducibility of findings between the included publications were limited, however, several studies validated the involvement of immune dysfunction in the pathology of ME/CFS and the use of lymphocytes as a model to investigate the pathomechanism of illness. The heterogeneity shown across many of the included studies highlights the need for multidisciplinary research and uniform protocols in ME/CFS biomarker research.

The practice of genomic medicine: A delineation of the process and its governing principles

Genomic medicine, an emerging medical discipline, applies the principles of evolution, developmental biology, functional genomics, and structural genomics within clinical care. Enabling widespread adoption and integration of genomic medicine into clinical practice is key to achieving precision medicine. We delineate a biological framework defining diagnostic utility of genomic testing and map the process of genomic medicine to inform integration into clinical practice. This process leverages collaboration and collective cognition of patients, principal care providers, clinical genomic specialists, laboratory geneticists, and payers. We detail considerations for referral, triage, patient intake, phenotyping, testing eligibility, variant analysis and interpretation, counseling, and management within the utilitarian limitations of health care systems. To reduce barriers for clinician engagement in genomic medicine, we provide several decision-making frameworks and tools and describe the implementation of the proposed workflow in a prototyped electronic platform that facilitates genomic care. Finally, we discuss a vision for the future of genomic medicine and comment on areas for continued efforts.

Starring Role of Biomarkers and Anticancer Agents as a Major Driver in Precision Medicine of Cancer Therapy

Precision medicine is the most modern contemporary medicine approach today, based on great amount of data on people's health, individual characteristics, and life circumstances, and employs the most effective ways to prevent and cure diseases. Precision medicine in cancer is the most precise and viable treatment for every cancer patient based on the disease's genetic profile. Precision medicine changes the standard one size fits all medication model, which focuses on average responses to care. Consolidating modern methodologies for streamlining and checking anticancer drugs can have long-term effects on understanding the results. Precision medicine can help explicit anticancer treatments using various drugs and even in discovery, thus becoming the paradigm of future cancer medicine. Cancer biomarkers are significant in precision medicine, and findings of different biomarkers make this field more promising and challenging. Naturally, genetic instability and the collection of extra changes in malignant growth cells are ways cancer cells adapt and survive in a hostile environment, for example, one made by these treatment modalities. Precision medicine centers on recognizing the best treatment for individual patients, dependent on their malignant growth and genetic characterization. This new era of genomics progressively referred to as precision medicine, has ignited a new episode in the relationship between genomics and anticancer drug development.

Association of Patient and Site-of-Care Characteristics With Reproductive Carrier Screening Timing in a Large Integrated Health System

IMPORTANCE

Reproductive genetic carrier screening can be performed prior to or during pregnancy to assess a reproductive couple's risk of having a child with a recessively inherited disorder. Although professional societies endorse preconception screening as preferable to prenatal screening to allow for greater reproductive choice, implementation of preconception screening is challenging.

OBJECTIVE

To determine how carrier screening timing varies by multilevel factors associated with health care delivery including patient, clinician, and location across a large integrated health care system.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study used a mixed-methods approach including (1) quantitative analysis of multilevel factors associated with the timing of reproductive carrier screening and (2) qualitative analyses of data from interviews conducted with clinicians ordering carrier screenings. The setting was the Mass General Brigham, a large integrated health care system in the greater Boston, Massachusetts area. Participants included adult female patients who completed reproductive carrier screening performed by Myriad Women's Health between October 1, 2018, to September 30, 2019.

EXPOSURES

Site of care (ordering clinical location and hospital affiliate), ordering clinician specialty, and patient characteristics, including age at date of test collection, self-reported race and ethnicity, primary insurance payor, and number of comorbidities.

MAIN OUTCOMES AND MEASURES

The primary outcome was the timing of carrier screening (preconception vs prenatal). A series of 4 multilevel logistic regression models were fitted to measure the relative contribution of site, clinician, and patient-level factors on the timing of screening. Interviews with ordering clinicians (N = 9) were analyzed using a framework approach to explore barriers to preconception screening.

RESULTS

Among 6509 adult female patients who completed carrier screenings, 770 (12%) were Asian, 352 (5%) were Hispanic, 640 (10%) were non-Hispanic Black, 3844 (59%) were non-Hispanic White, 858 (13%) were other or multiple races and ethnicities, and 2611 (40%) were aged 31 to 35 years; 4701 (63%) had prenatal screening and 2438 (37%) had preconception screening; screenings were ordered by 161 distinct clinicians across 32 clinical locations affiliated with 4 hospitals. In model 1, adjusted for hospital (fixed effect), clinic and clinician (random effects), 49% of the variability in timing was associated with clinician-level effects (intraclass correlation coefficient [ICC], 0.49) and 28% was associated with clinic-level effects (ICC, 0.28). Clinician specialty explained the greatest amount of variation in screening timing. Interviewed clinicians (N = 9) supported preconception screening but cited several barriers to offering population-based preconception screening.

CONCLUSIONS AND RELEVANCE

In this cross-sectional study, multilevel factors were associated with carrier screening timing. These findings suggest that increasing access to preconception screening may involve engaging specific medical specialties.

Detection of four rare thalassemia variants using Single-molecule realtime sequencing

Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --^27.3/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α^3.7α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination.

Psychosocial Effects of Receiving Genome-Wide Polygenic Risk Information Concerning Type 2 Diabetes and Coronary Heart Disease: A Randomized Controlled Trial

Receiving polygenic risk estimates of future disease through health care or direct-to-consumer companies is expected to become more common in the coming decades. However, only a limited number of studies have examined if such estimates might evoke an adverse psychosocial reaction in receivers. The present study utilized data from a sub-section of a personalized medicine project (the P5 study) that combines genomic and traditional health data to evaluate participants’ risk for certain common diseases. We investigated how communication of future disease risk estimates related to type 2 diabetes and coronary heart disease influenced respondents’ risk perception, self-efficacy, disease-related worry, and other emotions. A randomized controlled trial was conducted, where the experimental group (n = 714) received risk estimates based on traditional and polygenic risk factors and the control group (n = 649) based solely on traditional risk factors. On average, higher disease risk was associated with higher perceived risk (ps, <0.001, η_p² = 0.087–0.071), worry (ps <0.001, η_p² = 0.061–0.028), lower self-efficacy (p <0 .001, η_p² = 0.012), less positive emotions (ps <0.04, η_p² = 0.042–0.005), and more negative emotions (ps <0.048, η_p² = 0.062–0.006). However, we found no evidence that adding the polygenic risk to complement the more traditional risk factors would induce any substantive psychosocial harm to the recipients (ps >0.06).

Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing

Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PCR to uncover rare mutations in nine patients and their family members. The patients with different results between Gap-PCR and MMCA assay or with phenotype not matching genotype were included. Using SMRT sequencing, we first identified the carriers with ααα^anti3.7/HKαα, -α^762bpα/αα (chr16:172,648-173,409), αα^fusion/α^QSα (in a trans configuration), two cases with novel gene rearrangements and another case with a novel 341 bp insertion in α-globin gene cluster, respectively. One carrier with --^SEA/ααα^anti4.2, and two carriers with the coexistence of globin variant and an α-globin gene duplication were also found. Most importantly, we could determine two defects in α-globin gene cluster being a cis or trans configuration in a single test. Our results showed that SMRT has great advantages in detection of α-globin gene triplications, rare deletions and determination of a cis or trans configuration. SMRT is a comprehensive and one-step method for thalassemia screening and diagnosis, especially for detection of rare thalassemia mutations.

Using Long-Term Follow-Up Data to Classify Genetic Variants in Newborn Screened Conditions

With the rapid increase in publicly available sequencing data, healthcare professionals are tasked with understanding how genetic variation informs diagnosis and affects patient health outcomes. Understanding the impact of a genetic variant in disease could be used to predict susceptibility/protection and to help build a personalized medicine profile. In the United States, over 3.8 million newborns are screened for several rare genetic diseases each year, and the follow-up testing of screen-positive newborns often involves sequencing and the identification of variants. This presents the opportunity to use longitudinal health information from these newborns to inform the impact of variants identified in the course of diagnosis. To test this, we performed secondary analysis of a 10-year natural history study of individuals diagnosed with metabolic disorders included in newborn screening (NBS). We found 564 genetic variants with accompanying phenotypic data and identified that 161 of the 564 variants (29%) were not included in ClinVar. We were able to classify 139 of the 161 variants (86%) as pathogenic or likely pathogenic. This work demonstrates that secondary analysis of longitudinal data collected as part of NBS finds unreported genetic variants and the accompanying clinical information can inform the relationship between genotype and phenotype.

Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing

Background

Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workflows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input flexibility (1 ng-1 μg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits.

Results

We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits’ fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection.

Conclusions

The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quantabio are good alternatives to the tagmentation based Nextera DNA flex kit from Illumina, offering reproducible results using flexible DNA inputs, quick workflows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08316-y.

Psychosocial Effect of Newborn Genomic Sequencing on Families in the BabySeq Project: A Randomized Clinical Trial

IMPORTANCE

Newborn genomic sequencing (nGS) may provide health benefits throughout the life span, but there are concerns that it could also have an unfavorable (ie, negative) psychosocial effect on families.

OBJECTIVE

To assess the psychosocial effect of nGS on families from the BabySeq Project, a randomized clinical trial evaluating the effect of nGS on the clinical care of newborns from well-baby nurseries and intensive care units.

DESIGN, SETTING, AND PARTICIPANTS

In this randomized clinical trial conducted from May 14, 2015, to May 21, 2019, at well-baby nurseries and intensive care units at 3 Boston, Massachusetts, area hospitals, 519 parents of 325 infants completed surveys at enrollment, immediately after disclosure of nGS results, and 3 and 10 months after results disclosure. Statistical analysis was performed on a per-protocol basis from January 16, 2019, to December 1, 2019.

INTERVENTION

Newborns were randomized to receive either standard newborn screening and a family history report (control group) or the same plus an nGS report of childhood-onset conditions and highly actionable adult-onset conditions (nGS group).

MAIN OUTCOMES AND MEASURES

Mean responses were compared between groups and, within the nGS group, between parents of children who received a monogenic disease risk finding and those who did not in 3 domains of psychosocial impact: parent-child relationship (Mother-to-Infant Bonding Scale), parents' relationship (Kansas Marital Satisfaction Scale), and parents' psychological distress (Edinburgh Postnatal Depression Scale anxiety subscale).

RESULTS

A total of 519 parents (275 women [53.0%]; mean [SD] age, 35.1 [4.5] years) were included in this study. Although mean scores differed for some outcomes at singular time points, generalized estimating equations models did not show meaningful differences in parent-child relationship (between-group difference in adjusted mean [SE] Mother-to-Infant Bonding Scale scores: postdisclosure, 0.04 [0.15]; 3 months, -0.18 [0.18]; 10 months, -0.07 [0.20]; joint P = .57) or parents' psychological distress (between-group ratio of adjusted mean [SE] Edinburgh Postnatal Depression Scale anxiety subscale scores: postdisclosure, 1.04 [0.08]; 3 months, 1.07 [0.11]; joint P = .80) response patterns between study groups over time for any measures analyzed in these 2 domains. Response patterns on one parents' relationship measure differed between groups over time (between-group difference in adjusted mean [SE] Kansas Marital Satisfaction Scale scores: postdisclosure, -0.19 [0.07]; 3 months, -0.04 [0.07]; and 10 months, -0.01 [0.08]; joint P = .02), but the effect decreased over time and no difference was observed on the conflict measure responses over time. We found no evidence of persistent negative psychosocial effect in any domain.

CONCLUSIONS AND RELEVANCE

In this randomized clinical trial of nGS, there was no persistent negative psychosocial effect on families among those who received nGS nor among those who received a monogenic disease risk finding for their infant.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT02422511.

Genetic Risk Assessment for Atherosclerotic Cardiovascular Disease: A Guide for the General Cardiologist

Genetic testing for cardiovascular (CV) disease has had a profound impact on the diagnosis and evaluation of monogenic causes of CV disease, such as hypertrophic and familial cardiomyopathies, long QT syndrome, and familial hypercholesterolemia (FH). The success in genetic testing for monogenic diseases has prompted special interest in utilizing genetic information in the risk assessment of more common diseases such as atherosclerotic cardiovascular disease (ASCVD). Polygenic risk scores (PRS) have been developed to assess the risk of coronary artery disease (CAD) that now include millions of single-nucleotide polymorphisms (SNPs) that have been identified through genome-wide association studies (GWAS). While these PRS have demonstrated a strong association with CAD in large cross-sectional population studies, there remains intense debate regarding the added value that PRS contribute to existing clinical risk prediction models such as the pooled cohort equations (PCEs). In this review, we provide a brief background of genetic testing for monogenic drivers of CV disease and then focus on the recent developments in genetic risk assessment of ASCVD, including the use of PRS. We outline the genetic testing that is currently available to all cardiologists in the clinic and discuss the evolving sphere of specialized cardiovascular genetics programs (CVGPs) that integrate the expertise of cardiologists, geneticists, and genetic counselors. Finally, we review the possible implications that PRS and pharmacogenomic data may soon have on clinical practice in the care for patients with or at risk of developing ASCVD.

BioDWH2: an automated graph-based data warehouse and mapping tool

Data integration plays a vital role in scientific research. In biomedical research, the OMICS fields have shown the need for larger datasets, like proteomics, pharmacogenomics, and newer fields like foodomics. As research projects require multiple data sources, mapping between these sources becomes necessary. Utilized workflow systems and integration tools therefore need to process large amounts of heterogeneous data formats, check for data source updates, and find suitable mapping methods to cross-reference entities from different databases. This article presents BioDWH2, an open-source, graph-based data warehouse and mapping tool, capable of helping researchers with these issues. A workspace centered approach allows project-specific data source selections and Neo4j or GraphQL server tools enable quick access to the database for analysis. The BioDWH2 tools are available to the scientific community at https://github.com/BioDWH2.

Current scenario of the genetic testing for rare neurological disorders exploiting next generation sequencing

Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics, allowing for the detection of sequence variants with so far unprecedented large scale, mainly in genetically heterogenous diseases, such as neurological disorders. It is a fast-moving field, where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations. Despite the as yet undiscussed advantages, however, there are still some challenges in data analysis and the interpretation of variants. In this review, we address the current state of next generation sequencing diagnostic testing for inherited human disorders, particularly giving an overview of the available high-throughput sequencing approaches; including targeted, whole-exome and whole-genome sequencing; and discussing the main critical aspects of the bioinformatic process, from raw data analysis to molecular diagnosis.

From Theory to Reality: Establishing a Successful Kidney Genetics Clinic in the Outpatient Setting

Background

Genetic testing in nephrology is increasingly described in the literature and several groups have suggested significant clinical benefit. However, studies to date have described experience from established genetic testing centers or from externally funded research programs.

Methods

We established a de novo kidney genetics clinic within an academic adult general nephrology practice. Key features of this effort included a pipeline for internal referrals, flexible scheduling, close coordination between the nephrologist and a genetic counselor, and utilization of commercial panel-based testing. Over the first year, we examined the outcomes of genetic testing, the time to return of genetic testing, and out-of-pocket cost to patients.

Results

Thirty patients were referred and 23 were evaluated over the course of five clinic sessions. Nineteen patients underwent genetic testing with new diagnoses in nine patients (47%), inconclusive results in three patients (16%), and clearance for kidney donation in two patients (11%). On average, return of genetic results occurred 55 days (range 9-174 days) from the day of sample submission and the average out-of-pocket cost to patients was $155 (range $0-$1623).

Conclusions

We established a kidney genetics clinic, without a pre-existing genetics infrastructure or dedicated research funding, that identified a new diagnosis in approximately 50% of patients tested. This study provides a clinical practice model for successfully incorporating genetic testing into ambulatory nephrology care with minimal capital investment and limited financial effect on patients.

Family genetic result communication in rare and undiagnosed disease communities: Understanding the practice

Genetic results have implications not only for the individual, but also for their family members. Research on family communication of genetic results has primarily focused on families affected by adult-onset, dominant conditions as well as more common genetic conditions such as familial hypercholesterolemia, cardiomyopathies, and genetic hearing loss. This study therefore aimed to characterize genetic result communication in families with rare and undiagnosed conditions and identify factors that influence communication. One hundred and forty-two individuals who received a diagnosis from the Undiagnosed Diseases Network (UDN), a study focused on providing diagnoses to individuals with undiagnosed conditions, were eligible to complete a survey assessing genetic results communication. Survey items assessed if communication was discussed with healthcare providers, with whom participants communicated genetic testing, why they chose to communicate with these family members, and what information they communicated. All respondents (5 adult UDN participants, 38 parents/guardians of UDN participants, and 2 identifying as both) shared genetic results with at least one family member. Individuals who identified as both were considered exclusively adult participants for the purpose of these analyses. Adult participants and parents/guardians of participants reported high levels of understanding (96%), utility (96%), and comfort communicating genetic results (89%). Additionally, parents/guardians were more likely to disclose genetic results due to a general desire to share (60% of parents/guardians vs. 14% adult participants), while adult participants reported that they shared results to communicate risk to family members (86% of adult participants vs. 24% of parents/guardians). Many respondents did not recall discussing with a healthcare provider how (64%) or what (42%) to communicate about results. The results of this study provide insight into the practice of result communication by individuals with rare and previously undiagnosed conditions, which can ideally inform development of more effective counseling strategies and guidelines to aid family communication.

Knowing, relationships and trust-citizens' perceptions of whole genome sequencing for the Genetics Clinic of the Future

The objective of this article is to present various views from different groups of citizens on the topic of whole genome sequencing (WGS). Sixteen focus groups were carried out in Italy and Austria which aimed at reflecting on the question of how to ensure that the implementation of WGS into the clinic is relevant and responsive to the needs of all members of society. In the qualitative analysis of the focus groups, three key themes (knowing, relationships and trust) were investigated. Although the majority of the participants favoured a person-centred care approach, we also found more radical perspectives in the relationship theme. This includes a self-centred orientation in which health care institutions should be prepared to integrate self-interpretation efforts of citizens and develop strategies to deal with them. Different attitudes towards getting to know genetic information (knowing) and varied approaches to decision-making for or against the use of WGS were observed. Personal capacities, in particular those to handle medical information, were emphasized as key factors. This means that it is important not to connect the desire not to know with a rejection of the technology per se but rather to support information and consultancy processes that effectively involve citizens. Concerning the third theme, we have underlined the important role of mistrust in addition to trust because it mostly points to areas or conditions considered problematic. Thus, mistrust is also a way to articulate critique, for example, of the profit-making with patient data, that has to be taken seriously by governance.

Re-examining the Ethics of Genetic Counselling in the Genomic Era

Respect for patient autonomy has served as the dominant ethical principle of genetic counselling, but as we move into a genomic era, it is time to actively re-examine the role that this principle plays in genetic counselling practice. In this paper, we argue that the field of genetic counselling should move away from its emphasis on patient autonomy and toward the incorporation of a more balanced set of principles that allows counsellors to offer clear guidance about how best to obtain or use genetic information. We begin with a brief history of how respect for patient autonomy gained such emphasis in the field and how it has taken on various manifestations over time, including the problematic concept of nondirectiveness. After acknowledging the field's preliminary move away from nondirectiveness, we turn to a series of arguments about why the continued dominance of patient autonomy has become untenable given the arrival of the genomic era. To conclude, we describe how a more complete set of bioethical principles can be adapted and used by genetic counsellors to strengthen their practice without undermining patient autonomy.

Supercomputing and Secure Cloud Infrastructures in Biology and Medicine

The increasing amounts of healthcare data stored in health registries, in combination with genomic and other types of data, have the potential to enable better decision making and pave the path for personalized medicine. However, reaping the full benefits of big, sensitive data for the benefit of patients requires greater access to data across organizations and institutions in various regions. This overview first introduces cloud computing and takes stock of the challenges to enhancing data availability in the healthcare system. Four models for ensuring higher data accessibility are then discussed. Finally, several cases are discussed that explore how enhanced access to data would benefit the end user.

Genetic services diffusion in the precision medicine ecosystem

Purpose

Genetic knowledge is advancing steadily while at the same time DNA sequencing prices are dropping fast, but the diffusion of genetic services (GS) has been slow. The purpose of this paper is to identify GS diffusion drivers in the precision medicine (PM) ecosystem.

Design/methodology/approach

After reviewing the literature on innovation diffusion, particularly on GS diffusion, the PM ecosystem actors are interviewed to obtain their perspective. Using content analysis, the interviewees’ visions were interplayed with the literature to achieve driver conceptualization, which posteriorly originated broad themes.

Findings

The results indicate that GS diffusion depends on satisfying aspects from three broad themes and respective drivers: technology (evidence strength and credibility, customization, knowledge, data and information, tech evolution speed and cost), human (ethics, privacy and security and user power) and business (prevention, holistic view of the individual, public policy and regulation, business model and management).

Practical implications

The main management implications refer to considering health care in a multidisciplinary way, investing in the propagation of genetic knowledge, standardizing medical records and interpreting data.

Originality/value

This study, to the best of authors’ knowledge, is the first attempt to understand GS diffusion from a broad perspective, taking into account the PM stakeholders’ view. The 13 drivers offer a comprehensive understanding of how GS could spread in health care and they can assist researchers and practitioners to discuss and set strategies based on an initial structured map.

The State of Data Science in Genomic Nursing

Nurse scientists are generating, acquiring, distributing, processing, storing, and analyzing greater volumes of complex omics data than ever before. To take full advantage of big omics data, to address core biological questions, and to enhance patient care, however, genomic nurse scientists must embrace data science. Intended for readership with limited but expanding data science knowledge and skills, this article aims to provide a brief overview of the state of data science in genomic nursing. Our goal is to introduce key data science concepts to genomic nurses who participate at any stage of the data science lifecycle, from research patient recruitment to data wrangling, preprocessing, and analysis to implementation in clinical practice to policy creation. We address three major components in this review: (1) fundamental terminology for the field of genomic nursing data science, (2) current genomic nursing data science research exemplars, and (3) the spectrum of genomic nursing data science roles as well as education pathways and training opportunities. Links to helpful resources are included throughout the article.

Implementing the VMC Specification to Reduce Ambiguity in Genomic Variant Representation

Current methods used for representing biological sequence variants allow flexibility, which has created redundancy within variant archives and discordance among variant representation tools. While research methodologies have been able to adapt to this ambiguity, strict clinical standards make it difficult to use this data in what would otherwise be useful clinical interventions. We implemented a specification developed by the GA4GH Variant Modeling Collaboration (VMC), which details a new approach to unambiguous representation of variants at the allelic level, as a haplotype, or as a genotype. Our implementation, called the VMC Test Suite (http://vcfclin.org), offers web tools to generate and insert VMC identifiers into a VCF file and to generate a VMC bundle JSON representation of a VCF file or HGVS expression. A command line tool with similar functionality is also introduced. These tools facilitate use of this standard-an important step toward reliable querying of variants and their associated annotations.

Preserving Single Cells in Space and Time for Analytical Assays

Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.

Interactive or static reports to guide clinical interpretation of cancer genomics

Objective

Misinterpretation of complex genomic data presents a major challenge in the implementation of precision oncology. We sought to determine whether interactive genomic reports with embedded clinician education and optimized data visualization improved genomic data interpretation.

Materials and Methods

We conducted a randomized, vignette-based survey study to determine whether exposure to interactive reports for a somatic gene panel, as compared to static reports, improves physicians’ genomic comprehension and report-related satisfaction (overall scores calculated across 3 vignettes, range 0–18 and 1–4, respectively, higher score corresponding with improved endpoints).

Results

One hundred and five physicians at a tertiary cancer center participated (29% participation rate): 67% medical, 20% pediatric, 7% radiation, and 7% surgical oncology; 37% female. Prior to viewing the case-based vignettes, 34% of the physicians reported difficulty making treatment recommendations based on the standard static report. After vignette/report exposure, physicians’ overall comprehension scores did not differ by report type (mean score: interactive 11.6 vs static 10.5, difference = 1.1, 95% CI, −0.3, 2.5, P = .13). However, physicians exposed to the interactive report were more likely to correctly assess sequencing quality (P < .001) and understand when reports needed to be interpreted with caution (eg, low tumor purity; P = .02). Overall satisfaction scores were higher in the interactive group (mean score 2.5 vs 2.1, difference = 0.4, 95% CI, 0.2-0.7, P = .001).

Discussion and Conclusion

Interactive genomic reports may improve physicians’ ability to accurately assess genomic data and increase report-related satisfaction. Additional research in users’ genomic needs and efforts to integrate interactive reports into electronic health records may facilitate the implementation of precision oncology.

Patient Dossier: Healthcare queries over distributed resources

As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain greatly hinders these developments, including ethical and legal issues, fragmentation of the relevant data in different locations, and a level of (meta)data complexity that requires great expertise across technical, clinical, and biological domains. We propose the Patient Dossier paradigm as a way to organize new innovative healthcare services that sorts the current limitations. The Patient Dossier conceptual framework identifies the different issues and suggests how they can be tackled in a safe, efficient, and responsible way while opening options for independent development for different players in the healthcare sector. An initial implementation of the Patient Dossier concepts in the Rbbt framework is available as open-source at https://github.com/mikisvaz and https://github.com/Rbbt-Workflows.

Value of Collaboration among Multi-Domain Experts in Analysis of High-Throughput Genomics Data

The recent explosion and ease of access to large-scale genomics data is intriguing. However, serious obstacles exist to the optimal management of the entire spectrum from data production in the laboratory through bioinformatic analysis to statistical evaluation and ultimately clinical interpretation. Beyond the multitude of technical issues, what stands out the most is the absence of adequate communication among the specialists in these domains. Successful interdisciplinary collaborations along the genomics pipeline extending from laboratory experiments to bioinformatic analyses to clinical application are notable in large scale, well managed projects such as The Cancer Genome Atlas. However, in certain settings in which the various experts perform their specialized research activities in isolation, the siloed approach to their research contributes to the generation of questionable genomic interpretations. Such situations are particularly concerning when the ultimate endpoint involves genetic/genomic interpretations that are intended for clinical applications. In spite of the fact that clinicians express interest in gaining a better understanding of clinical genomic applications, the lack of communication from upstream experts leaves them with a serious level of discomfort in applying such genomic knowledge to patient care. This discomfort is especially evident among healthcare providers who are not trained as geneticists, in particular primary care physicians. We offer some initiatives that have potential to address this problem, with emphasis on improved and ongoing communication among all the experts in these fields, constituting a comprehensive genomic "pipeline" from laboratory to patient.

The influence of a solvent on the electronic transport across diamondoid-functionalized biosensing electrodes

Electrodes embedded in nanopores have the potential to detect the identity of biomolecules, such as DNA. This identification is typically being done through electronic current measurements across the electrodes in a solvent. In this work, using quantum-mechanical calculations, we qualitatively present the influence of this solvent on the current signals. For this, we model electrodes functionalized with a small diamond-like molecule known as diamondoid and place a DNA nucleotide within the electrode gap. The influence of an aqueous solvent is taken explicitly into account through Quantum-Mechanics/Molecular Mechanics (QM/MM) simulations. From these, we could clearly reveal that at the (111) surface of the Au electrode, water molecules form an adlayer-like structure through hydrogen bond networks. From the temporal evolution of the hydrogen bond between a nucleotide and the functionalizing diamondoid, we could extract information on the conductance across the device. In order to evaluate the influence of the solvent, we compare these results with ground-state electronic structure calculations in combination with the non-equilibrium Green's function (NEGF) approach. These allow access to the electronic transport across the electrodes and show a difference in the detection signals with and without the aqueous solution. We analyze the results with respect to the density of states in the device. In the end, we demonstrate that the presence of water does not hinder the detection of a mutation over a healthy DNA nucleotide. We discuss these results in view of sequencing DNA with nanopores.

Clonal Hematopoiesis: Crossroads of Aging, Cardiovascular Disease, and Cancer: JACC Review Topic of the Week

A novel, common, and potent cardiovascular risk factor has recently emerged: clonal hematopoiesis of indeterminate potential (CHIP). CHIP arises from somatic mutations in hematopoietic stem cells that yield clonal progeny of mutant leukocytes in blood. Individuals with CHIP have a doubled risk of coronary heart disease and ischemic stroke, and worsened heart failure outcomes independent of traditional cardiovascular risk factors. The recognition of CHIP as a nontraditional risk factor challenges specialists in hematology/oncology and cardiovascular medicine alike. Should we screen for CHIP? If so, in whom? How should we assess cardiovascular risk in people with CHIP? How should we manage the excess cardiovascular risk in the absence of an evidence base? This review explains CHIP, explores the clinical quandaries, strives to provide reasonable recommendations for the multidisciplinary management of cardiovascular risk in individuals with CHIP, and highlights current knowledge gaps.

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing.

Consent for clinical genome sequencing: considerations from the Clinical Sequencing Exploratory Research Consortium

Implementing genome and exome sequencing in clinical practice presents challenges, including obtaining meaningful informed consent. Consent may be challenging due to test limitations such as uncertainties associated with test results and interpretation, complexity created by the potential for additional findings and high patient expectations. We drew on the experiences of research teams within the Clinical Sequencing Exploratory Research (CSER1) Consortium on informed consent for clinical genome and exome sequencing (CGES) to negotiate consensus considerations. We present six considerations for clinicians and 12 key points to communicate as they support patients in deciding whether to undergo CGES. These considerations and key points provide a helpful starting point for informed consent to CGES, grounded in the Clinical Sequencing Exploratory Research (CSER1) experience.

Use of genetic risks in pediatric organ transplantation listing decisions: A national survey

There is a limited supply of organs for all those who need them for survival. Thus, careful decisions must be made about who is listed for transplant. Studies show that manifesting genetic disease can impact listing eligibility. What has not yet been studied is the impact genetic risks for future disease have on a patient's chance to be listed. Surveys were emailed to 163 pediatric liver, heart, and kidney transplant programs across the United States to elicit views and experiences of key clinicians regarding each program's use of genetic risks (ie, predispositions, positive predictive testing) in listing decisions. Response rate was 42%. Sixty-four percent of programs have required genetic testing for specific indications prior to listing decisions. Sixteen percent have required it without specific indications, suggesting that genetic testing may be used to screen candidates. Six percent have chosen not to list patients with secondary findings or family histories of genetic conditions. In hypothetical scenarios, programs consider cancer predispositions and adult-onset neurological conditions to be relative contraindications to listing (61%, 17%, and 8% depending on scenario), and some consider them absolute contraindications (5% and 3% depending on scenario). Only 3% of programs have formal policies for these scenarios, but all consult genetic specialists at least "sometimes" for results interpretation. Our study reveals that pediatric transplant programs are using future onset genetic risks in listing decisions. As genetic testing is increasingly adopted into pediatric medicine, further study is needed to prevent possible inappropriate use of genetic information from impacting listing eligibility.

Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans

Despite of the low occurrence rate in the entire genomes, de novo mutation is proved to be deleterious and will lead to severe genetic diseases via impacting on the gene function. Considering the fact that the traditional family based linkage approaches and the genome-wide association studies are unsuitable for identifying the de novo mutations, in recent years, several pipelines have been proposed to detect them based on the whole-genome or whole-exome sequencing data and were used for calling them in the rare diseases. However, how the performance of these variant calling pipelines on detecting the de novo mutations is still unexplored. For the purpose of facilitating the appropriate choice of the pipelines and reducing the false positive rate, in this study, we thoroughly evaluated the performance of the commonly used trio calling methods on the detection of the de novo single-nucleotide variants (DNSNVs) by conducting a comparative analysis for the calling results. Our results exhibited that different pipelines have a specific tendency to detect the DNSNVs in the genomic regions with different GC contents. Additionally, to refine the calling results for a single pipeline, our proposed filter achieved satisfied results, indicating that the read coverage at the mutation positions can be used as an effective index to identify the high-confidence DNSNVs. Our findings should be good support for the committees to choose an appropriate way to explore the de novo mutations for the rare diseases.

The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders

Structural variation, composed of balanced and unbalanced genomic rearrangements, is an important contributor to human genetic diversity with prominent roles in somatic and congenital disease. At the nucleotide level, structural variants (SVs) have been shown to frequently harbor additional breakpoints and copy-number imbalances, a complexity predicted to emerge wholly as a single-cell division event. Chromothripsis, chromoplexy, and chromoanasynthesis, collectively referred to as chromoanagenesis, are three major mechanisms that explain the occurrence of complex germline and somatic SVs. While chromothripsis and chromoplexy have been shown to be key signatures of cancer, chromoanagenesis has been detected in numerous cases of developmental disease and phenotypically normal individuals. Such observations advocate for a deeper study of the polymorphic and pathogenic properties of complex germline SVs, many of which go undetected by traditional clinical molecular and cytogenetic methods. This review focuses on congenital chromoanagenesis, mechanisms leading to occurrence of these complex rearrangements, and their impact on chromosome organization and genome function. We highlight future applications of routine screening of complex and balanced SVs in the clinic, as these represent a potential and often neglected genetic disease source, a true "iceberg under water."

Parental interest in genomic sequencing of newborns: enrollment experience from the BabySeq Project

PURPOSE

Newborn genomic sequencing (nGS) has great potential to improve pediatric care. Parental interest and concerns about genomics are relatively unexplored. Understanding why parents decline research consent for nGS may reveal implementation barriers.

METHODS

We evaluated parental interest in a randomized trial of nGS in well-baby and intensive care unit nursery settings. Interested families attended an informational enrollment session (ES) with a genetic counselor prior to consenting. Reason(s) for declining participation and sociodemographic associations were analyzed.

RESULTS

Of 3860 eligible approached families, 10% attended ES, 67% of whom enrolled. Of 1760 families queried for decline reasons, 58% were uninterested in research. Among 499 families considering research, principal reasons for decline prior to ES included burdensome study logistics (48%), feeling overwhelmed postpartum (17%), and lack of interest/discomfort with genetic testing (17%). Decliners after ES more often cited concerns about privacy/insurability (41%) and uncertain/unfavorable results (23%).

CONCLUSION

Low interest in research and study logistics were major initial barriers to postpartum enrollment and are likely generic to many postpartum research efforts. Concerns over privacy and result implications were most commonly cited in decliners after ES. Understanding parental concerns around research nGS may inform future integration of nGS into newborn screening, predictive testing, and pediatric diagnostics.

Genomic Interventions in Medicine

Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.

Genetic and Genomic Consultation: Are We Ready for Direct-to-Consumer Telegenetics?

Telegenetics, the application of telemedicine in the context of genetic services, is a growing market. One of the recent developments in this field is the use of direct-to-consumer (DTC) marketing to promote and advertise genetic and genomic consultant services to consumers. Using Google.com, we identified providers that promote their telegenetics services online. By analyzing their websites, we identify and examine key points regarding DTC telegenetics: how are telegenetics services portrayed, how is informed consent obtained, and what protections are offered to clients' personal health information? We found that the portrayal of a wide range of telegenetics services on providers' websites is extremely positive. The risks associated with the implementation of telegenetics were rarely mentioned. Consent forms were often unavailable and did not cover all of the relevant information. The measures for protecting clients' personal health information by telegenetics providers were found to be generally inadequate and weak. We concluded that DTC telegenetics may increase patients' access to genetic counseling with affordable costs. However, before further developing DTC telegenetics, more research and regulatory improvements are required to guarantee truthful advertising, ensure informed consent, secure personal health data sharing, and warrant adequate privacy protection.