PMID- 30275890
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201001
IS  - 1753-6561 (Print)
IS  - 1753-6561 (Electronic)
IS  - 1753-6561 (Linking)
VI  - 12
IP  - Suppl 9
DP  - 2018
TI  - Analysis of genotype by methylation interactions through sparsity-inducing 
      regularized regression.
PG  - 40
LID - 10.1186/s12919-018-0145-6 [doi]
LID - 40
AB  - In this paper, we consider the use of the least absolute shrinkage and selection 
      operator (LASSO)-type regression techniques to detect important genetic or 
      epigenetic loci in genome-wide association studies (GWAS) and epigenome-wide 
      association studies (EWAS). We demonstrate how these techniques can be adapted to 
      provide quantifiable uncertainty using stability selection, including explicit 
      control of the family-wise error rate. We also consider variants of the LASSO, 
      such as the group LASSO, to study genetic and epigenetic interactions. We use 
      these techniques to reproduce some existing results on the Genetics of Lipid 
      Lowering Drugs and Diet Network (GOLDN) data set, which collects from 991 
      individuals blood triglyceride and differential methylation at 464,000 
      cytosine-phosphate-guanine (CpG) sites and 761,000 single-nucleotide 
      polymorphisms (SNPs), and to identify new research directions. Epigenome-wide and 
      genome-wide models based on the LASSO are considered, as well as an interaction 
      model limited to chromosome 11. The analyses replicate findings concerning 2 CpGs 
      in carnitine palmitoyltransferase 1A (CPT1A). Some suggestions are made regarding 
      potentially interesting directions for the analysis of genetic and epigenetic 
      interactions.
FAU - Zhou, Wenda
AU  - Zhou W
AD  - Department of Statistics, Columbia University, 1255 Amsterdam Avenue, New York, 
      NY 10027 USA. ISNI: 0000000419368729. GRID: grid.21729.3f
FAU - Lo, Shaw-Hwa
AU  - Lo SH
AD  - Department of Statistics, Columbia University, 1255 Amsterdam Avenue, New York, 
      NY 10027 USA. ISNI: 0000000419368729. GRID: grid.21729.3f
LA  - eng
GR  - R01 GM031575/GM/NIGMS NIH HHS/United States
GR  - R01 HL091357/HL/NHLBI NIH HHS/United States
GR  - R01 HL104135/HL/NHLBI NIH HHS/United States
GR  - U01 HL072524/HL/NHLBI NIH HHS/United States
PT  - Journal Article
DEP - 20180917
PL  - England
TA  - BMC Proc
JT  - BMC proceedings
JID - 101316936
PMC - PMC6157158
COIS- Not applicable.Not applicable.The authors declare that they have no competing 
      interests.Springer Nature remains neutral with regard to jurisdictional claims in 
      published maps and institutional affiliations.
EDAT- 2018/10/03 06:00
MHDA- 2018/10/03 06:01
PMCR- 2018/09/17
CRDT- 2018/10/03 06:00
PHST- 2018/10/03 06:00 [entrez]
PHST- 2018/10/03 06:00 [pubmed]
PHST- 2018/10/03 06:01 [medline]
PHST- 2018/09/17 00:00 [pmc-release]
AID - 145 [pii]
AID - 10.1186/s12919-018-0145-6 [doi]
PST - epublish
SO  - BMC Proc. 2018 Sep 17;12(Suppl 9):40. doi: 10.1186/s12919-018-0145-6. eCollection 
      2018.