A clinical hereditary cancer population screening initiative, called Information is Power, began in North Alabama in 2015. After 4 years of the initiative, we were interested in exploring (1) the characteristics and motivations for patients who self-refer to population genetic testing, (2) how patients make decisions on testing, (3) what patients do with results, and (4) patient perceptions of benefits and limitations after undergoing population genetic testing. Patients who consented to research recontact at time of test ordering were sent an electronic survey with the option for a follow-up phone interview. Among the 2,918 eligible patients, 239 responded to the survey and 19 completed an interview. Survey and interview participants were highly educated information seekers motivated by learning more about their health. Those who were previously interested in hereditary cancer testing reported barriers were cost and insurance coverage, access to testing, and uncertainty how results could impact their health. Many participants (77%) communicated with family and friends about their decision to test and communicated about test results. Fewer participants (23%) discussed the decision to test with their healthcare providers; however, 58% of participants discussed their test results with a healthcare provider. Most people (96%) with negative results accurately recalled their results. In contrast, three out of 11 positive results for heterozygous MUTYH, PALB2, and BRCA2 reported receiving negative results. This study contributes to knowledge on population genetic testing and may guide other population genetic testing programs as they develop enrollment materials and educational materials and consider downstream needs of population genetic testing participants.

Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has challenged the speed at which laboratories can discover the viral composition and study health outcomes. The small ∼30-kb ssRNA genome of coronaviruses makes them adept at cross-species spread while enabling a robust understanding of all of the proteins the viral genome encodes. We have employed protein modeling, molecular dynamics simulations, evolutionary mapping, and 3D printing to gain a full proteome- and dynamicome-level understanding of SARS-CoV-2. We established the Viral Integrated Structural Evolution Dynamic Database (VIStEDD at RRID:SCR_018793) to facilitate future discoveries and educational use. Here, we highlight the use of VIStEDD for nsp6, nucleocapsid (N), and spike (S) surface glycoprotein. For both nsp6 and N, we found highly conserved surface amino acids that likely drive protein–protein interactions. In characterizing viral S protein, we developed a quantitative dynamics cross-correlation matrix to gain insights into its interactions with the angiotensin I–converting enzyme 2 (ACE2)–solute carrier family 6 member 19 (SLC6A19) dimer. Using this quantitative matrix, we elucidated 47 potential functional missense variants from genomic databases within ACE2/SLC6A19/transmembrane serine protease 2 (TMPRSS2), warranting genomic enrichment analyses in SARS-CoV-2 patients. These variants had ultralow frequency but existed in males hemizygous for ACE2. Two ACE2 noncoding variants (rs4646118 and rs143185769) present in ∼9% of individuals of African descent may regulate ACE2 expression and may be associated with increased susceptibility of African Americans to SARS-CoV-2. We propose that this SARS-CoV-2 database may aid research into the ongoing pandemic.

Cystic Fibrosis (CF) is caused most often by removal of amino acid 508 (Phe508del, deltaF508) within CFTR, yet dozens of additional CFTR variants are known to give rise to CF and many variants in the genome are known to contribute to CF pathology. To address CFTR coding variants, we developed a sequence-to-structure-to-dynamic matrix for all amino acids of CFTR using 233 vertebrate species, CFTR structure within a lipid membrane, and 20 ns of molecular dynamic simulation to assess known variants from the CFTR1, CFTR2, ClinVar, TOPmed, gnomAD, and COSMIC databases. Surprisingly, we identify 18 variants of uncertain significance within CFTR from diverse populations that are heritable and a likely cause of CF that have been understudied due to nonexistence in Caucasian populations. In addition, 15 sites within the genome are known to modulate CF pathology, where we have identified one genome region (chr11:34754985-34836401) that contributes to CF through modulation of expression of a noncoding RNA in epithelial cells. These 15 sites are just the beginning of understanding comodifiers of CF, where utilization of eQTLs suggests many additional genomics of CFTR expressing cells that can be influenced by genomic background of CFTR variants. This work highlights that many additional insights of CF genetics are needed, particularly as pharmaceutical interventions increase in the coming years.

The SARS-CoV-2 pandemic, starting in 2019, has challenged the speed at which labs perform science, ranging from discoveries of the viral composition to handling health outcomes in humans. The small ~30kb single-stranded RNA genome of Coronaviruses makes them adept at cross species spread and drift, increasing their probability to cause pandemics. However, this small genome also allows for a robust understanding of all proteins coded by the virus. We employed protein modeling, molecular dynamic simulations, evolutionary mapping, and 3D printing to gain a full proteome and dynamicome understanding of SARS-CoV-2. The Viral Integrated Structural Evolution Dynamic Database (VIStEDD) has been established (prokoplab.com/vistedd), opening future discoveries and educational usage. In this paper, we highlight VIStEDD usage for nsp6, Nucleocapsid (N), and Spike (S) surface glycoprotein. For both nsp6 and N we reveal highly conserved surface amino acids that likely drive protein-protein interactions. In characterizing viral S protein, we have developed a quantitative dynamics cross correlation matrix insight into interaction with the ACE2/SLC6A19 dimer complex. From this quantitative matrix, we elucidated 47 potential functional missense variants from population genomic databases within ACE2/SLC6A19/TMPRSS2, warranting genomic enrichment analyses in SARS-CoV-2 patients. Moreover, these variants have ultralow frequency, but can exist as hemizygous in males for ACE2, which falls on the X-chromosome. Two noncoding variants (rs4646118 and rs143185769) found in ~9% of African descent individuals for ACE2 may regulate expression and be related to increased susceptibility of African Americans to SARS-CoV-2. This powerful database of SARS-CoV-2 can aid in research progress in the ongoing pandemic.

As genomic sequencing expands, so does our knowledge of the link between genetic variation and disease. Deeper catalogs of variant frequencies improve identification of benign variants, while sequencing affected individuals reveals disease-associated variation. Accumulation of human genetic data thus makes reanalysis a means to maximize the benefits of clinical sequencing. We implemented pipelines to systematically reassess sequencing data from 494 individuals with developmental disability. Reanalysis yielded pathogenic or likely pathogenic (P/LP) variants that were not initially reported in 23 individuals, 6 described here, comprising a 16% increase in P/LP yield. We also downgraded 3 LP and 6 variants of uncertain significance (VUS) due to updated population frequency data. The likelihood of identifying a new P/LP variant increased over time, as ~22% of individuals who did not receive a P/LP variant at their original analysis subsequently did after 3 years. We show here that reanalysis and data sharing increase the diagnostic yield and accuracy of clinical sequencing.

Truncating mutations including frameshift mutations and nonsense mutations contribute to ~45% of all mutations leading to NF1. However, the extent to which specific mechanisms are involved in causing these mutations has not been well explored yet. Here, we analyzed the frequency and characteristics of 1,924 and 1,731 NF1 individuals carrying frameshift and nonsense mutations respectively out of a total number of ~8,100 unrelated NF1 mutationpositive probands from the University of Alabama at Birmingham Medical Genomics Laboratory and inferred their likely mutational mechanisms. Interestingly, eight frameshift mutation hotspots were identified, which were associated with non-B DNA structures and short tandem repeats. On the other hand, 18 nonsense mutation hotspots were identified, which all occurred at CpG dinucleotides. Furthermore, it is believed that a termination codon must reside further than 5055 nucleotides upstream of the splice donor of the penultimate exon, for nonsense-mediated mRNA be able to decay the transcripts. However, no constitutional truncating mutations beyond c.8154 were found in our cohort, nor have been described in other disease-associated datasets, which is 160 nucleotides before the exon 57 end, suggesting truncating mutations downstream of c.8154 may not result in an NF1 phenotype.

Background: Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-parent trios.Methods: Whole-exome sequences (WES) were generated for 365 individuals (127 affected) and whole-genome sequences (WGS) were generated for 612 individuals (244 affected).Results: Pathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11.3%). We found that a family history of neurological disease, especially the presence of an affected first-degree relative, reduces the pathogenic/likely pathogenic variant identification rate, reflecting both the disease relevance and ease of interpretation of de novo variants. We also found that improvements to genetic knowledge facilitated interpretation changes in many cases. Through systematic reanalyses, we have thus far reclassified 15 variants, with 11.3% of families who initially were found to harbor a VUS and 4.7% of families with a negative result eventually found to harbor a pathogenic or likely pathogenic variant. To further such progress, the data described here are being shared through ClinVar, GeneMatcher, and dbGaP.Conclusions: Our data strongly support the value of large-scale sequencing, especially WGS within proband-parent trios, as both an effective first-choice diagnostic tool and means to advance clinical and research progress related to pediatric neurological disease.

Life science classrooms often emphasize the exception to the rule when it comes to teaching genetics, focusing heavily on rare single-gene and Mendelian traits. By contrast, the vast majority of human traits and diseases are caused by more complicated interactions between genetic and environmental factors. Research indicates that students have a deterministic view of genetics, generalize Mendelian inheritance patterns to all traits, and have unrealistic expectations of genetic technologies. The challenge lies in how to help students analyze complex disease risk with a lack of curriculum materials. Providing open access to both content resources and an engaging storyline can be achieved using a “serious game” model. “Touching Triton” was developed as a serious game in which students are asked to analyze data from a medical record, family history, and genomic report in order to develop an overall lifetime risk estimate of six common, complex diseases. Evaluation of student performance shows significant learning gains in key content areas along with a high level of engagement.

Life science classrooms often emphasize the exception to the rule when it comes to teaching genetics, focusing heavily on rare single-gene and Mendelian traits. By contrast, the vast majority of human traits and diseases are caused by more complicated interactions between genetic and environmental factors. Research indicates that students have a deterministic view of genetics, generalize Mendelian inheritance patterns to all traits, and have unrealistic expectations of genetic technologies. The challenge lies in how to help students analyze complex disease risk with a lack of curriculum materials. Providing open access to both content resources and an engaging storyline can be achieved using a "serious game" model. "Touching Triton" was developed as a serious game in which students are asked to analyze data from a medical record, family history, and genomic report in order to develop an overall lifetime risk estimate of six common, complex diseases. Evaluation of student performance shows significant learning gains in key content areas along with a high level of engagement.

Research Article| April 01 2014 Genetics in the Classroom: Instruction & Enthusiasm Neil E. Lamb Neil E. Lamb 1HudsonAlpha Institute for Biotechnology Search for other works by this author on: This Site PubMed Google Scholar The American Biology Teacher (2014) 76 (4): 220–221. https://doi.org/10.1525/abt.2014.76.4.1 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Neil E. Lamb; Genetics in the Classroom: Instruction & Enthusiasm. The American Biology Teacher 1 April 2014; 76 (4): 220–221. doi: https://doi.org/10.1525/abt.2014.76.4.1 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe American Biology Teacher Search I am a science educator because of people like Frances Bowman. Miss Bowman taught seventh-grade science at a junior high school outside Chattanooga, Tennessee. She was my teacher in the early 1980s. We covered a lot of ground in that class: Miss Bowman taught her students a form of shorthand so that our note taking could keep pace with her lecture speed. Once a week, the lectures took a backseat to labs. I had been raised with an appreciation of science, but one of these sessions brought biology into focus as a real career possibility. It was a classic activity: peering through a microscope at a drop of pond water. The thriving community of tiny creatures captured my imagination like nothing before. Looking back, I believe that the taxonomy of biology was what initially attracted me to the field – as an awkward teen who felt completely out of place,... You do not currently have access to this content.

The Biotechnology Discoveries and Applications guidebook aims to provide teachers with an overview of the recent advances in genetics and biotechnology, allowing them to share these findings with their students. The annual guidebook introduces a wealth of modern genomic discoveries and provides teachers with tools to integrate exciting content into the classroom. Released annually by the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama, the guidebook presents new findings in jargon-free, student-friendly language. The guidebook is introduced along with strategies for classroom use.

The Biotechnology Discoveries and Applications guidebook aims to provide teachers with an overview of the recent advances in genetics and biotechnology, allowing them to share these findings with their students. The annual guidebook introduces a wealth of modern genomic discoveries and provides teachers with tools to integrate exciting content into the classroom. Released annually by the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama, the guidebook presents new findings in jargon-free, student-friendly language. The guidebook is introduced along with strategies for classroom use.

Advances in genomics have enabled any individual to examine his or her own genetic information and have increased the desire for medical care tailored to one’s own genome. Yet, many practicing physicians are uncomfortable with, or unable to, incorporate genetic information into the relevant areas of care. In this chapter, we review problems and existing solutions, and offer recommendations for changes to medical school curricula and continuing education.

Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

Recent advances in research and biotechnology are making genetics and genomics increasingly relevant to the lives and health of the general public. For the public to make informed healthcare and public policy decisions relating to genetic information, there is a need for increased genetic literacy. Biotech 101 is a free, short-course for the local community introducing participants to topics in genetics, genomics, and biotechnology, created at the HudsonAlpha Institute for Biotechnology. This study evaluated the effectiveness of Biotech 101 in increasing the genetic literacy of program participants through pre-and-post surveys. Genetic literacy was measured through increases in self-perceived knowledge for each content area covered through the course and the self-reported impact the course had on various aspects of participants' lives. Three hundred ninety-two individuals attended Biotech 101 during the first three course offerings. Participants reported a significant increase in self-perceived knowledge for each content area (p < 0.01). Participants also reported the program had high levels of impact on their lives and decision-making, a high likelihood for continued self-learning, and overwhelming satisfaction with course content and logistics. Biotech 101 is an effective mechanism for impacting participants' lives and genetic literacy and serves as a model for other similar programs, adding to the currently limited evidence base regarding public educational strategies in genetics and biotechnology.

We describe the implementation of “APPLE for the Teacher,” an alternative education outreach program that augments teacher efforts in presenting specific AP Biology laboratory exercises and at the same time involves the community in the educational process. The program is 5 years old and is staffed primarily by volunteers. We discuss the experiences of participants and lessons learned during the program’s implementation and growth.

Where do members of the public turn to understand what genetic tests mean in terms of their own health? Now that genome-wide association studies and complete genome sequencing are widely available, the importance of education in personalized genomics cannot be overstated. Although some media have introduced the concept of genetic testing to better understand health and disease, the public's understanding of the scope and impact of genetic variation has not kept up with the pace of the science or technology. Unfortunately, the likely sources to which the public turn to for guidance - their physician and the media - are often no better prepared. We examine several venues for information, including print and online guides for both lay and health-oriented audiences, and summarize selected resources in multiple formats. We also note on the roadblocks to progress and discuss ways to remove them, as urgent action is needed to connect people with their genomes in a meaningful way.

Advancing maternal age has long been identified as the primary risk factor for human chromosome trisomy. More recently, altered patterns of meiotic recombination have been found to be associated with non-disjunction. We have used trisomy 21 as a model for human non-disjunction that occurs during the formation of oocytes to understand the role of maternal age and recombination. Patterns of recombination that increase the risk for non-disjunction of chromosome 21 include absence of any exchange, an exchange near the centromere or a single, telomeric exchange. Our recent work has shown that different susceptibility patterns are associated with the origin of the meiotic error and maternal age. For MI (meiosis I) errors, the proportion of oocytes with susceptible recombination patterns is highest among young mothers and decreases significantly in the oldest age group. In fact, the pattern of exchanges among the oldest age group mimics the pattern observed among normally disjoining chromosomes 21. These results suggest that oocytes of younger women, with functional meiotic apparatus and/or robust ovarian environment, are able to properly resolve all but the most susceptible exchange patterns. As women age, however, meiotic mechanisms erode, making it difficult to resolve even stable exchange events. Interestingly, our preliminary recombination results on MII errors reveal the opposite relationship with maternal age: susceptible pericentromeric exchanges occur most often in the older age group compared with the younger age group. If confirmed, we will have further evidence for multiple risk factors for non-disjunction that act at different times in the meiotic process.