News And Notes From ASHG 2018

October 23, 2018 | The American Society of Human Genetics (ASHG) hosted their annual meeting last week in San Diego, California. Here are some of the announcements made during the meeting.

10x Genomics announced availability of several products announced earlier this year. Chromium Single Cell ATAC Solution is the first launched product to come out of the company's recent acquisition of Epinomics. It is also the first commercially-available solution for rapid and massively parallel profiling of single cell epigenomic signatures. The solution includes comprehensive software that enables rapid analysis and visualization of large-scale single cell ATAC-seq experiments. Feature Barcoding technology, and a suite of certified compatible products, enables simultaneous analysis of a specific biological component of interest together with either unbiased gene expression or immune profiles within that same cell. The technology can support a wide variety of research applications depending upon which biological component is being targeted, and can include cell surface proteins, T cell receptors, CRISPR-mediated perturbations, or other targets of interest to the researcher. The new technology will be offered as a ready-to-use commercial solution, in contrast to published homebrew methods like CITE-seq, REAP-seq, Perturb-seq, and CROP-seq. Finally, the company announced significant enhancements to its flagship product for single cell transcriptomics, the Chromium Single Cell Gene Expression Solution. Press release

DNAnexus has announced DNAnexus Apollo, an enhanced platform for clinico-genomic data science exploration, analysis, and discovery, allowing R&D teams to rapidly test multiple hypotheses and gain valuable insight into mechanisms of action, biomarkers, and targets. DNAnexus Apollo provides a scalable cloud environment, flexible data models, and intuitive analysis and visualization tools to simplify research workflows for R&D teams globally. Working with clinical data requires specialized capabilities to maintain privacy, DNAnexus Apollo leverages the same best-in-class DNAnexus security and privacy framework, which includes compliance in accordance with HIPAA, CLIA, GxP, and FedRAMP, among others.

Geneticists have assembled the largest sets of African genomic data available to date according to research presented by the Wellcome Sanger Institute. The effort creates a resource that will help researchers understand the genetic structure of Africa as well as the effects of genetic variation on protein function and disease. The researchers collected and analyzed genome-wide data from 6,400 individuals from rural Uganda, including the whole genome sequences of 1,978 people within that group. They combined this with data from an additional 7,784 individuals from other African countries, in the first genome-wide association study (GWAS) to analyze multiple traits across Africa. Press release

By combining data on individuals’ lifetime sun exposure and their genetics, researchers can generate improved predictions of their risk of skin cancer, according to findings presented by 23andMe. Company researchers collected genetic and survey data from over 210,000 consented research participants of European descent. Past studies had found that exposure to ultraviolet (UV) light increases skin cancer risk, as do other environmental factors such as living in a sunnier climate or at a higher altitude, and personal factors such as lighter skin pigmentation, higher numbers of moles on the skin, and family history of skin cancer. The new researcher found that while each single factor was not particularly significant on its own, multiple factors could be combined into statistical models that were more informative. Press release

Helix announced a new DNA Product Studio designed for partners to easily develop and distribute DNA products. Helix’s DNA Product Studio will allow partners to bring innovative new products to the Helix marketplace in a matter of weeks, from concept to launch. The new platform builds on Helix's growing library of hundreds of genomic insights, traits and conditions, allowing partners to create compelling experiences for individuals. The partner platform tools will help Helix’s partners leverage the power of DNA to personalize their existing products, build new ones, and pioneer new avenues for preventive health, all of which will benefit millions of people who are interested in learning about how DNA plays a role in health, wellness and beyond. DNA Product Studio includes: the Ancestry API: Continental Ancestry for 6 global populations, or regional ancestry for 26+ populations; the Insight API: User-specific results for hundreds of genetic traits or conditions. Options range from simple, single-marker traits to complex polygenic risk scores using thousands of markers and machine learning-based scoring models; and the Genomics API, which gives direct access to more than 100 million base pairs, including SNPs, indels, and copy number variants. Press release

Comprehensive genetic testing of tumors and non-cancerous tissue from pediatric cancer patients is a feasible and clinically useful approach that can guide patient care, according to an interdisciplinary team at St. Jude Children’s Research Hospital. The researchers studied 253 pediatric oncology patients with a variety of cancers. In 79% of cases, there was at least one finding that could help guide care by providing a diagnosis, revealing patient-specific risks, or identifying drug targets. The researchers conducted whole genome sequencing (WGS), whole exome sequencing (WES), and RNA sequencing of the patients’ tumors, as well as WGS and WES of non-cancerous tissue from the same patient. The team developed software pipelines and analysis methods to identify the most clinically relevant variants. Most of their findings were structural rearrangements of DNA within or between chromosomes, and thus would have been challenging to detect (or not detected at all) using other, less comprehensive methods. With an eye to implementation, the researchers showed that this comprehensive testing would not overburden the analysis process, and that information could be provided within about 40 days, a time frame short enough to be of clinical value. The data are available on the St. Jude Cloud. Press release

Bionano Genomics and Genoox announced the launch of the Genoox Integrated Platform for identification of structural variants. By using Genoox technology for aligning short read sequence data with Bionano’s structural variant (SV) calls, the high sensitivity of Bionano calls will be combined with the base pair precision of NGS. The Genoox Integrated Platform automatically validates and confirms SV calls and integrates and annotates SVs with smaller sequence variants in the same genome. It provides sensitive, accurate detection of structural variation and genetic mutations, not previously possible, helping to speed genetic diagnosis. The new platform combines raw NGS read data with Bionano-based SV calls from a single patient. Bionano’s SV data are used to guide the alignment of NGS reads. Evidence from both technologies is used simultaneously to provide increased breakpoint accuracy and confidence. Detected SVs, copy number variants, indels and single nucleotide variants are then annotated by aggregating data from multiple clinical and population frequency databases, and automated AI-based classification according to ACMG guidelines. A customizable clinical report on all variants is generated, including Bionano-only and NGS-only calls, reducing the complexity of determining and reporting the pathogenicity of genomic variants. Press release

Fabric Genomics and Genomenon have entered into an agreement to integrate and co-market their solutions. Fabric Genomics speeds and scales genomic interpretation by combining the most advanced AI algorithms with automated workflows, while Genomenon’s literature search engine facilitates comprehensive literature review, which is advantageous for accurate interpretation. The integration between Fabric Enterprise and Mastermind will allow users to see which candidate variants have any related scientific literature entries, with direct access to a prioritized list of relevant articles during variant interpretation and classification. Press release