Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4.

Following publication of the original article [1], the author explained that Table 2 is displayed incorrectly. The correct Table 2 is given below. The original article has been corrected.

Recommendations for performance optimizations when using GATK3.8 and GATK4.

Background: Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computational performance improvements have been introduced in GATK3.

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy.

As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy.

Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing.

Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient's genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse.

Thiopurine S-methyltransferase pharmacogenetics: variant allele functional and comparative genomics.

Thiopurine S-methyltransferase (TPMT) catalyses the S-methylation of thiopurine drugs. Genetic polymorphisms for TPMT are a major factor responsible for large individual variations in thiopurine toxicity and therapeutic effect. The present study investigated the functional effects of human TPMT variant alleles that alter the encoded amino acid sequence of the enzyme, TPMT*2, *3A, *3B, *3C and *5 to *13.

Translating pharmacogenomics discoveries into clinical practice: the role of curated databases.

Pharmacogenomics-related genotype information is growing at a supra-linear rate, and phenotype-related information, as determined by computer simulations, in vitro experiments and clinical studies, is also growing. Even when phenotypic information is confirmed via clinical research, numerous barriers exist in translating these discoveries into clinical practice. We consider two of them here: the uncertainty regarding the practical relevance of research observations, and translation of significant research findings into clinical practice and research through electronic information access.

Human cytosolic sulfotransferase database mining: identification of seven novel genes and pseudogenes.

A total of 10 SULT genes are presently known to be expressed in human tissues. We performed a comprehensive genome-wide search for novel SULT genes using two different but complementary approaches, and developed a novel graphical display to aid in the annotation of the hits. Seven novel human SULT genes were identified, five of which were predicted to be pseudogenes, including two processed pseudogenes and three pseudogenes that contained introns.

Designing and implementing special-purpose databases: lessons from the pharmacogenetic network.

The Pharmacogenetics Research Network, which has the long-term goal of genotype-phenotype correlation related to pharmacotherapy, mandates timely electronic publication of results by participating research groups through submission to PharmGKB, the consortium's repository database. Because informatics expertise across groups varies, many groups need help in managing their own data and in generating electronic submissions. To assist these operations, we perform a needs assessment to determine an optimum database implementation strategy, which varies from standalone microcomputer database application to Web-based solutions, depending on the group and problem scope.