Advanced Whole Genome Sequencing and Analysis of Fetal Genomes from Amniotic Samples

Amniocentesis is a procedure that collects cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single to multi-base defects. However, it is blind to birth defects known to be caused by single to megabase scale changes in thousands of different genes and chromosomal regions. In an effort to improve the detection of the number of birth defects by this test we apply whole genome sequencing to 30 amniocentesis samples. For all samples cell free DNA (cfDNA), isolated from the amniotic fluid, and DNA isolated from the cell pellet, were sequenced to ~50X genome coverage using complete genomics nanoarray platform. In a subset of the samples, Long Fragment Read (LFR) libraries were generated from DNA isolated from cells and sequenced to ~100X genome coverage. DNA isolated from the blood of each parent was sequenced to ~50X on the same platform for all amniotic samples. In total... (for more see dbGaP study page.)