The 64th annual meeting of the American Society of Human Genomics was held October 18–22 in San Diego, California. The event attracted 8,433 attendees, including 6,566 scientific attendees (nonexhibitors), a 3.1% decrease from the 2013 show, which was held in Boston, Massachusetts. Two hundred forty companies exhibited, compared with 235 last year.

In a Tuesday session entitled “Exome Sequencing as a Standard of Care in Clinical Genomics,” Sumit Muddha, an informatics specialist at the Mayo Clinic, reported on a study that sought to correlate whole-exome sequencing (WES) results with clinical findings in an effort to identify the predictive nature of clinical sequencing. The presentation highlighted the challenges of correlating genomic and phenotypic information based on WES. The exomes of 89 deceased individuals were sequenced. Diagnoses of each individual were made by a medical geneticist based on electronic medical records. A total of 7,046 variants were identified after filtering, or about 79 per person, but for only 3% was evidence for the variants found in their phenotypes, while 53% showed no phenotypic correlation. However, 23% of phenotypes had matching genotypes. The study highlighted several limitations to predictive sequencing, including pseudogenes (nonfunctional genomic sequences), sequence homology, missing coverage and variant-filtering thresholds.

Informatics, including data sharing, was a topic addressed in multiple presentations. As part of a Tuesday session, Dave Kaufman, PhD, director of Research and Statistics of the Genetics and Public Policy Center at Johns Hopkins University, presented the results of a survey of human geneticists about their use of the NIH’s dbGaP database of genotypes and phenotypes. Last spring’s survey of genetic researchers, dbGaP contributors and dbGaP applications garnered 357 responses. The results indicated the importance of data sharing and its challenges. Although 73% of respondents cited data sharing (defined as the use of others’ research data and samples) as more important over the past five years, 12% stated that sharing their own data conflicted with advancing their careers. Seventy-five percent of respondents used some data collected directly by their team, and 90% used some data collected by other researchers. However, 25% used only data and samples collected by others. And even though 84% of respondents support the requirement that federally funded researchers submit data to dbGaP, over 24% said they would not submit data if it was not a requirement. In fact, 23% disagreed with the statement, “I trust secondary researchers to treat data and samples responsibly”, and 44% think that genetic data is occasionally shared inappropriately.

ASHG 2014 was also an important venue for next-generation sequencing (NGS)–based studies. Pacific Biosciences’s single-molecule–sequencing technologies was the focus of multiple presentations. In a talk entitled “Increased Complexity of the Human Genome Revealed by Single-molecule Sequencing,” Mark Chaisson, PhD, of the University of Washington discussed the sequencing of the naturally haploid hydatidiform mole CHM1 using Pacific Biosciences’ PacBio RS II sequencer and P5-3C chemistry at 40x coverage. The project is part of an NIH effort to create an alternate reference genome. The average mapped read length was 5.8 kbp. Eighty-five percent of the detected structural variants were novel compared to previous studies, and the average variant length was 497 bp. He noted that inversions were detected with high specificity.

Debuting at the show was Pacific Bioscience’s latest chemistry and software for its PacBio RS II DNA Sequencing System. The P6-C4 chemistry enables average read lengths of 10,000–15,000 bases, compared with the previous read length of 8.5 kb on average. Half of the data in the reads are now over 14,000 bases in length, compared with half of the data in reads of 10 kb with P5-C3, the previous chemistry, and the longest read is over 40,000 bases.

Several companies highlighted new target-enrichment products. Integrated DNA Technologies introduced xGen Predesigned Gene Capture Pools and Plates for customized target-capture panels for enrichment of 10 or more genes using its XGen Lockdown Probes. The preordered panels are available with a separate gene in each well of a plate or as a mixed gene pool, allowing several researchers to customize their experiments in-house. The format also allows for pooling with other manufacturers’ panels. The cost is $100 per gene for 16 reactions in a plate or pool and $150 per gene for 96 reactions.

Illumina launched the HiSeq X HD v2 Reagents Kits, which now support its TruSeq DNA PCR-Free Sample Preparation Kit. For the HiSeq 2500 systems, the company introduced the HiSeq Rapid v2 Reagent Kit for generating longer read lengths. The new kit enables 2 x 250 bp, paired-end reads, which improves accuracy for applications such as complex metagenomics and de novo assembly. At Roche NimbleGen’s booth, the company highlighted its target-enrichment kits, including custom arrays for clinical applications. The company plans to release the SeqCap RNA kit for targeted sequencing shortly.

At the show, Agilent Technologies launched the SureSelect Focused Exome target-enrichment solution for disease-associated regions for 20 or more reads at 95% of targets at 1.5 Gb. It is designed for use with the SureSelectQXT Reagent Kit. SureSelectQXT was released in June and features a total time to sequencer of seven hours, according to the company. The SureSelect Focused Exome provides 20 or more reads for 95% of targets at 100x sequencing. It can be run on benchtop sequencers.

Agilent also displayed the new open-platform AriaMx Real-Time PCR System. The modular design accommodates up to six slots for individual optical cartridges for multiplexing from two to six channels. The system is initially available with four or five cartridges, with more cartridges to be introduced later. It features high-resolution melt capabilities.

Thermo Fisher Scientific showed Life Technologies’ Symphoni cloud-based data-analysis software for secondary analysis of results generated by selected Life Technologies qPCR and Sanger-sequencing systems. SymphoniqPCR is scheduled to launch in November. The beta version of SymphoniSanger is currently out, with the QC module as the first-available module. Data storage for SymphoniqPCR will be available starting in November 2015. The CloudSuite environment will offer 10 GB of complimentary storage.

For its digital PCR system, Thermo released the QuantStudio 3D Rare Mutation Analysis Solution for 38 common mutations in cancer genes. It includes 40 TaqMap SNP genotyping assays. The company also displayed its Arcturus LCM system dual-laser–capture microdissection system, which can be used to obtain samples for NGS. Applications include sequencing of single neurons.

Fluidigm launched its early-access program for its Juno system. Designed for its production-genomics customers who are working with difficult samples, Juno enables a lower sample input, requiring only 5.5 ng of DNA at a concentration of 2.5 ng per µL of sample. Ninety-six samples and 96 assays can be processed on one chip in under three hours, according to the company.

PerkinElmer displayed its LabChip Gx Touch for Genomics 24, a low-throughput addition to its line of microfluidic-based capillary electrophoresis systems, which was introduced earlier this year. It processes up to 24 samples, and the chips can be reused for up to 50 samples. The instrument features a smaller footprint and easier serviceability than the LabChip GX, as well as a new touchscreen. It is priced at $55,000.

Bio-Rad Laboratories introduced the QX200 Automated Droplet Generator for its Droplet Digital PCR system. The liquid handler generates and plates 96 PCR droplets in about 40 minutes, according to the company. This compares to manual droplet generation for up to eight droplets. The company also launched the CFX Automation II plate handler for its PCR system, which can service two systems.

ASHG 2015 will be held October 6–10 in Baltimore, Maryland.