Butte Lab Journal Club 4/25/11

1. Butte Lab Journal Club4/25/11 Linda Liu

3. Ethnic differences in survival after childhood ALL have been reported in many clinical studies, with poorer survival observed among African Americans or those with Hispanic ethnicity when compared with European Americans or Asians. Results: Did PCA on germline SNP genotypes, and found that the component of variation associated with Native American ancestry also associated with risk of relapse. Adding a single phase of chemo eliminated ancestry-related differences.

4. PCA analysis of genome-wide germline SNP genotypes in children with ALL PC1: African ancestry PC2: East Asian ancestry PC3: Native American ancestry

5. a) Genetic ancestral composition of 2500 children with ALL. Each patient is a column. Red: European, Gray: African, Green: Asian, Blue: Native American Higher levels of NA ancestry associated with risk of relapse in b) all patients, c) self-reported white, d) patients without extra dose of chemo d) Differences disappeared among patients given extra dose of chemo

6. Used 22 sequenced fecal metagenomes of individuals from 4 countries to identify 3 robust clusters (enterotypes) that are not nation or continent specific • Confirmed the enterotypes in 2 published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous • Functional modules can be identified for each of these host properties. 12 genes significantly correlate with age, 3 functional modules with BMI

8. Sequencing Applications

9. Hannah Valantine is a transplant surgeon at Stanford who also works on sex differences in cardiovascular disease • She approached Quake to use his sequencing technology on cell-free DNA in transplant patients • They found that an increase in the amount of the donor’s DNA in the recipient’s blood is one of the earliest detectable signs of organ rejection • A simple blood draw may soon replace the regular surgical biopsies that are currently used to track the health of the donor heart “Heart transplant recipients undergo at least 12 tissue biopsies during the first year after their transplant and two or three each year for about four additional years” – Hannah Valantine “This approach, we call genome transplant dynamics (GTD)” – Stephen Quake

10. Easiest to pick out donor DNA from polymorphic sequences where the recipient’s two copies did not differ, but at least one of the donor’s genes varied

11. Rejection episodes corresponded to levels of donor DNA of 3-4 percent When the patients were treated with immunosuppressants, the amount of the donor DNA decreased to <1% A) Female receiving male heart, with acute rejection B) Female receiving male heart, no rejection C) Male receiving male heart, with acute rejection

12. 10% of cell-free DNA in maternal plasma is of fetal origin • But this is enough for next-gen sequencing technology to sequence fragments and assemble into full genetic map, using parent genomes as guides • Can then scan fetal genome for mutations, noninvasively

13. Used massively parallel sequencing to sequence maternal plasma to 65-fold coverage • Depth of coverage of fetal allele relative to all reads • Sequencing depth across whole genome • - Green: GC content • Maternal and fetal genomes present at constant proportions, with distinct fragmentation patterns

14. Proof-of-concept study in a family where both parents carry mutations for blood disease thalassemia (autosomal recessive disease, symptoms: severe anemia) • See if fetus carries 0, 1, or 2 mutations • Found that fetus carried paternal mutation, but not maternal mutation

15. It has previously been hypothesized that X-linked genes are expressed at twice the level of autosomal genes per active allele to balance the gene dose between the X chromosome and autosomes Microarray-based gene expression levels were indistinguishable between one X chromosome and two autosomes RNA sequencing (RNA-Seq) is more sensitive than microarray and that RNA-Seq data reveal an X:AA ratio of ~0.5 in human and mouse

17. RNA-seq median expression of autosomal genes (circles) and X-linked genes (diamonds) X:AA ratios of median expression in human liver

18. Preterm Birth

19. One reason for pre-term birth relates to natural selection acting on the opposing forces of large head size and narrow birth canal • Larger brain = good for fetal survival but deadly to mother • Genes involved in birth timing have faster evolution in human lineages and promote delivery of smaller fetus • Screened 8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers • Most significant association was in FSHR (follicle stimulating hormone receptor) • Confirmed in African Americans • Identifying “at risk” genomic profiles can be very important information when it comes to allocation of finite medical resources.

22. - Women with lupus (SLE) or otherautoimmune conditions characterized by complement-mediated injury have increased risk of preeclampsia • and miscarriage • PROMISSE= prospective study of 250 pregnant patients with SLE • Sequenced genes encoding three complement regulatory proteins—membrane cofactor protein (MCP), complement factor I (CFI), and complement factor H (CFH)—in 40 patients who had preeclampsia and found heterozygous mutations in seven (18%) • Confirmed MCP and CFI association in non-autoimmune PE patients