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Biology subjects

Imran S Haque

Publications and source records attributed to Imran S Haque.

3 recordsLinked to original sources

Clinical Utility of Expanded Carrier Screening: Reproductive Behaviors of At-Risk Couples

PurposeExpanded carrier screening (ECS) analyzes dozens or hundreds of recessive genes for determining reproductive risk. Data on clinical utility of screening conditions beyond professional guidelines is scarce.\n\nMethodsIndividuals underwent ECS for up to 110 genes. 537 at-risk couples (ARC), those in which both partners carry the same recessive disease, were invited to a retrospective IRB-approved survey of their reproductive decision making after receiving ECS results.\n\nResults64 eligible ARC completed the survey. Of 45 respondents screened preconceptionally, 62% (n=28) planned IVF with PGD or prenatal diagnosis (PNDx) in future pregnancies. 29% (n=13) were not planning to alter reproductive decisions. The remaining 9% (n=4) of responses were unclear.\n\nOf 19 pregnant respondents, 42% (n=8) elected PNDx, 11% (n=2) planned amniocentesis but miscarried, and 47% (n=9) considered the condition insufficiently severe to warrant invasive testing. Of the 8 pregnancies that underwent PNDx, 5 were unaffected and 3 were affected. 2 of 3 affected pregnancies were terminated.\n\nDisease severity was found to have significant association (p=0.000145) with changes in decision making, whereas guideline status of diseases, controlled for severity, was not (p=0.284).\n\nConclusionMost ARC altered reproductive planning, demonstrating the clinical utility of ECS. Severity of conditions factored into decision making.

Genetics

SSCM: A method to analyze and predict the pathogenicity of sequence variants

AbstractThe advent of cost-effective DNA sequencing has provided clinics with high-resolution information about patients genetic variants, which has resulted in the need for efficient interpretation of this genomic data. Traditionally, variant interpretation has been dominated by many manual, time-consuming processes due to the disparate forms of relevant information in clinical databases and literature. Computational techniques promise to automate much of this, and while they currently play only a supporting role, their continued improvement for variant interpretation is necessary to tackle the problem of scaling genetic sequencing to ever larger populations. Here, we present SSCM-Pathogenic, a genome-wide, allele-specific score for predicting variant pathogenicity. The score, generated by a semi-supervised clustering algorithm, shows predictive power on clinically relevant mutations, while also displaying predictive ability in noncoding regions of the genome.

Bioinformatics

A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD

The bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a 3 x N x N x 3 matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3 x N case that are able to significantly outperform (by up to 3X) off-the-shelf high-performance linear algebra libraries for this computation, reaching machine limits on performance. The routines are implemented in C and Python libraries, and are available at https://github.com/simtk/IRMSD.

Biophysics