Redin:Large-insert jumping library, median insert 3.7kb. '11 AJHG ref http://t.co/FOy4z37H7K #ASHG15
9:39am October 10th 2015 via Hootsuite
Redin: Also to look at genes involved with BCA mechanism. n=176. Majority of BCA: 63% cognitive impaired #ASHG15
9:38am October 10th 2015 via Hootsuite
Redin: BCA - balanced Cr abnormality, invisible to most microarrays. Built a BCA sequencing consortium; mechanism for de novo BCA #ASHG15
9:37am October 10th 2015 via Hootsuite
Claire Redin (Mass Gen Hosp) Char de novo balanced cytogenetic abnormalities by sequencing 147 w/multiple congenital anomalies #ASHG15
9:36am October 10th 2015 via Hootsuite
Jeremian:Q:Other populations? A:No plans, haplogroup is highly preserved though. #ASHG15
9:33am October 10th 2015 via Hootsuite
Jeremian:Q:What about protein level? A:Not measured, only mRNA levels #ASHG15
9:32am October 10th 2015 via Hootsuite
Jeremian: Suggesting epigenetics may model how genetic risk factors increase (or decrease) over time. ASHG15
9:30am October 10th 2015 via Hootsuite
Jeremian: Their lincRNA: called LOC, modulates LCT. Model: Epigenetics depending on haplotype, affecting expression temporally. #ASHG15
9:29am October 10th 2015 via Hootsuite
Jeremian: Used CRISP-Cas9 to remove Mcm6 intron 13, Lct intron 2, with decreases in mRNA levels. #ASHG15
9:26am October 10th 2015 via Hootsuite
Jeremian: In mice: conserved intron 2 region, also found in other mammals. LCT intron 2: an 'old regulator' for MCM6 region #ASHG15
9:25am October 10th 2015 via Hootsuite
Jeremian: DNA modification density heat-map: seeing haplotype-specific trends over time. "Genotype-dep temporal epigenetic change' #ASHG15
9:24am October 10th 2015 via Hootsuite
Jeremian: The cell-specificity: found a lincRNA. 6/7 regions were DNAse hypersensitive, and active histone marks #ASHG15
9:22am October 10th 2015 via Hootsuite
Jeremian: Looked at 900 CpG's in that region, found inter-individual differences related to expression. Enterocyte cell-type - why? #ASHG15
Jeremian: Sample collection - had to look at lining where cells express LCT gene. Found LCT exon1 intron 1 correlation to exp. #ASHG15
9:21am October 10th 2015 via Hootsuite
Jeremian: Collected 115 human jejunum smpls, chr2 DNA modifications; bisulfite mappig, replicated in CRISPR-mod mice #ASHG15
9:20am October 10th 2015 via Hootsuite
Jeremian: Most common: chr2-13910C/T (C=intolerance, T=persist). Why LCT decreases w/age? And connection to genome? -> epigenetics #ASHG1
9:19am October 10th 2015 via Hootsuite
Jeremian: Persistence in pastoral, recently-evolved population-spec SNPs, and example of convergent evolution #ASHG15
9:18am October 10th 2015 via Hootsuite
Jeremian: About 70% humans are lactose-intolerant; consumed in the large intestine by bacteria. 30%: lactase persistent. #ASHG15
9:17am October 10th 2015 via Hootsuite
Jeremian: First weeks, our survival depends on the ability to metabolize milk. Lactase - LCT; exp mRNA decreases #ASHG15
9:16am October 10th 2015 via Hootsuite
Ritchie Jeremian (U Toronto): Genetic and epigenetic factors affecting regulatory elements underlie lactose intolerance #ASHG15
9:15am October 10th 2015 via Hootsuite
RT @edyong209: On Thu, I told the #ASHG15 attendees that science journalism should be a corrective force. Well... http://t.co/ck8F6Qc6EP
9:09am October 10th 2015 via Hootsuite
Andolina: Concl: a high yield of non-BRCA1/2 pathogenic in women with br ca. Evidence that it should be an initial test in diagnosis #ASHG15
6:26pm October 9th 2015 via Hootsuite
Andolina: Moderate risk: newer genes were much lower freq. BRIP1(37), FANCC (25) etc #ASHG15
6:25pm October 9th 2015 via Hootsuite
Andolina: 29/1395 had TP53; others in high-risk genes had personal or family history features. CHEK2 (350), ATM(150) and PALB2(120) #ASHG15
6:24pm October 9th 2015 via Hootsuite
Andolina: Limited by the information they receive though. Colon ca genes: 5% in Lynch syndrome genes; also picked up 3 polyposis pos #ASHG15
6:22pm October 9th 2015 via Hootsuite
Andolina: Long tail of genes in high-risk: MSH6, TP53, PMS2. Chart: 20% no family history, 75% did. 20% history of ov ca #ASHG15
6:21pm October 9th 2015 via Hootsuite
Andolina: 15K women w/breast cancer; 1.3K (8.9%) detected. 35 with >1 PV/LPV. 36% (501/1395) in BRCA1/2. #ASHG15
6:20pm October 9th 2015 via Hootsuite
Andolina: Limited studies on hereditary cancer testing with a broader range of genes. GeneDx started Aug '13, 6-29 genes #ASHG15
6:17pm October 9th 2015 via Hootsuite
Laura Andolina (GeneDx) Yield of pathogenic/likely pathogenic variants in women w/ breast cancer & hereditary cancer panel testing #ASHG
6:16pm October 9th 2015 via Hootsuite
.@thatdnaguy Safe travels - great to meet IRL!
6:12pm October 9th 2015 via Hootsuite in reply to thatdnaguy
Campbell: Q:Able to compare to ExAC? A:They did, matched pretty well in general. But some are very rare #ASHG15
6:12pm October 9th 2015 via Hootsuite
Campbell: However: a small but clinically impt group of gene families - PALB2, TP53, PTEN, CDH1. GOUS=genes of unk significance #ASHG15
6:10pm October 9th 2015 via Hootsuite
Campbell: Data indicate many genes included in commercial panels 'do not conform to current guidelines' #ASHG15
6:09pm October 9th 2015 via Hootsuite
Campbell: 'Demand for more extensive gen testing should not compromise obligation to apply robust principles of test development' #ASHG15
6:08pm October 9th 2015 via Hootsuite
Campbell: Looking at data by gene (ex-PALB2 and TP53) most are equal in cases as controls. RAD50 tho is weak evidence: more in ctrls #ASHG15
6:07pm October 9th 2015 via Hootsuite
Campbell: Populated adjusted risk: 2.4%, relatively low (given samples x genes). More than 1/2 PALB2 and TP53 #ASHG15
6:04pm October 9th 2015 via Hootsuite
Campbell: 85 in cases, 46 in controls. Found add'l BRCA1/2 in controls (at about expected freq) #ASHG15
6:03pm October 9th 2015 via Hootsuite
Campbell: 18 genes, full exons, of 3,994 total 202 truncating vars, 665 rare missense. Of these: 131 apparently pathogenic #ASHG15
6:02pm October 9th 2015 via Hootsuite
Campbell: Targeted exon seq of br ca predisposition genes, HaloPlex, HiSeq2500 and BWA. Large chart of genes and providers #ASHG15
6:01pm October 9th 2015 via Hootsuite
Campbell: Took 2K index cases HBOC families, 1,997 controls from 'http://t.co/F4Kev35LYU'; healthy women in br ca screening #ASHG15
6:00pm October 9th 2015 via Hootsuite
Campbell: Highly active area of research but 'limited critical assessment'. Large chart of BRCA studies, but 'no WT controls' #ASHG15
5:59pm October 9th 2015 via Hootsuite
Campbell: The problem: no consensus on list of genes that should be included, or technical / clinical intepretation #ASHG15
5:58pm October 9th 2015 via Hootsuite
Ian Campbell (Melbourne, AUS) Panel testing for familial breast cancer: Tension at the boundary of research and clinical care #ASHG15
5:57pm October 9th 2015 via Hootsuite
Bodian: 'WGS is complementary to NBS'; WGS can pinpoint the molecular basis, will need to be periodically re-evaluated #ASHG15
5:34pm October 9th 2015 via Hootsuite
Bodian: 4-39 VUS. Limit to 65 genes in state of VA. Preterm neonates have more samples collected, but didn't affect positive rate #ASHG15
5:31pm October 9th 2015 via Hootsuite
Bodian: Made results available online in this recent ref http://t.co/JPHE28L0gR #ASHG15
5:29pm October 9th 2015 via Hootsuite
Bodian: Used CGI for first, ILMN for the second. Look for 163 NBS genes. Assigned pathogenicity scores; predicted status #ASHG15
5:28pm October 9th 2015 via Hootsuite
Bodian: WGS isn't 'whole genome', are newborn screening genes detectable? Have n-732, w/ 1/3 preterm. And n=964 '1000d of life' #ASHG15
5:27pm October 9th 2015 via Hootsuite
Dale Bodian (Inova) Utility of WGS for detection of newborn screening disorders in a population cohort of 1696 neonates #ASHG15
5:25pm October 9th 2015 via Hootsuite
Naik:Retrospective analysis sent for genetic testing; n=1245; by specialty and by age (majority 20 - 64yo). #ASHG15
5:17pm October 9th 2015 via Hootsuite
