not invented here.

Notes on bioinformatics methods, software and discussions.

posts tagged “pediatrics”:

9.21.2011 Next generation clinical sequencing in a children’s hospital

Stephen Kingsmore - Children’s Mercy Hospital in Kansas City, USA

OMIM lists ~7000 inherited diseases, 3-4% affect children, for half the molecular basis is unknown. Exome sequencing helps to elucidate causes for others and leads to reclassification of common complex diseases. Large number of different inheritance patterns (autosomal recessive, X-linked, dominant, mitochondrial, imprinting disorders, …). About 1000 diseases with sufficient knowledge for molecular testing [Paging @phylogenomics.. Mendelianome?]. Typical diagnosis one at a time sanger sequencing, newborn screening of ~60 treatable conditions (1-3$/test), pre-conception carrier testing.

FDA-approved process or CLIA laboratory, sequencing not an approved process yet (see Mark Boguski’s talk); patent processes another quagmire (BRCA1/2).

A need for mendelian genomic medicine with multiple concepts:

  • Testing the mendelianome
  • Newborn screening for ~120 treatable disorders
  • Preconception carrier testing for a similar set of disorders
  • Fetal diagnosis and treatment
  • Pharmacogenome testing before treatment

NGS-based clinical sequencing is very different to Sanger-based molecular diagnostics. Multi-plexing is obligatory to achieve economic efficiency (multiple disease tests, samples at the same time), turnaround as low as four weeks. Exome-seq as a research tool too expensive still for diagnostic purposes, too high a risk of missing exons, poor handling of GC-rich regions. Ultimate approach WGS once price becomes reasonable to avoid inefficiencies of capture methods.

Outline of a standardized NGS screen for 619 inherited diseases. Counseling, blood sample, enrich 0.1% of genome, sequence around 4GB, genotype, report differences, results report and counseling. Need to take ethics into account (do not check for variants not specifically requested). Around 3 million dollar investment (1/3 IT infrastructure, 96-well semi-automated system). Custom library for Illumina TruSeq; HiSeq 2000 running 96 samples in 5 days, ~95% of targets have > 16X coverage sufficient for clinical diagnostic.

Need to translate alignments into allele frequency to reliably distinguish heterozygous and homozygous calls, cannot undercall these. Tweaked sequencing depth and enrichment technology until in 99.99% specificity, 96% sensitivity. Interpretation can be automated (90%, 9% manual, 1% case conference as aim). Despite of three decades of variant annotation no workflow to identify benign/pathologic variants (mentioned a few times before).

[Skipping sample cases as I got distracted, ahem…]

Much of the current literature-cited mutations (~20%) disease mutations are common SNPs or falsely annotated. Echoes previous calls for a clinical-grade variant database; ClinVar at NIH is one such initiative.

"Circle of hopelessness": paltry funding for rare diseases, limiting testing and therapies, little known about the mutations, lack of ascertainment or timely diagnosis, limited therapeutic options. Try to tackle collective compile large disease burden to raise collective R&D funding, generate comprehensive genetic testing, improve diagnosis and therapy.

Conference ✳ beyond the genome ✳ sequencing ✳ pediatrics