Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

5 March 2019

Pooled-parent exome sequencing to diagnose de novo genetic diseases

Harriet Dashnow
MCRI

In the clinical setting, exome sequencing has become instrumental in diagnosing rare genetic disorders, however many cases still remain unsolved. This is in part because sequencing produces a large number of candidate variants and it may be difficult to determine which variant is causing the disease at hand. One strategy shown to increase the diagnostic yield is to additionally sequence the parents of the patient. This is called trio sequencing. Knowing which variants are also found in the parents can be used to prioritise those that best fit the observed pattern of inheritance. Trio sequencing has been demonstrated to produce a higher diagnostic yield than singleton (proband-only) sequencing. Sequencing the parents is especially useful when a disease is suspected to be caused by a de novo variant in the proband, because the parents become a strong filter to remove the majority of variants that are shared by both. However the additional cost of sequencing the parents makes the trio strategy uneconomical for many projects. With two thirds of the sequencing budget being spent on parents, these are funds that could be used to sequence more probands. For this reason many clinics are reluctant to sequence parents.

Here we propose a pooled-parent strategy for exome sequencing of individuals with likely de novo disease. In this strategy, DNA from all the parents of a set of probands is pooled together and then we perform a single exome capture and sequencing run. Variants called in the proband can then be filtered if they are also found in the parent pool, resulting in a shorter list of prioritised variants. To evaluate the pooled-parent strategy we performed a series of simulations by combining reads from individual exomes to imitate sample pooling. We assessed the recall and false positive rate and investigated the trade-off between pool size, recall rate and cost. We compared the performance of GATK HaplotypeCaller and FreeBayes to genotype pooled samples. Finally, we applied a pooled-parent strategy to a set of real unsolved cases from MCRI and showed that the parent pool is a powerful filter that is complementary to other commonly used variant filters such as population variant frequencies.


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