A multiomics project

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case study

MS

Asthma

SLE

VitD

Gaps

OBJECTIVES

2. Proteomics expression of Vit D deficiency

1. Identify genetic mechanism of Vit D defiency

CASE STUDY: VITAMIN D & CALCIUM

Step 5: Check X levels in lab results, questionnaires, EMR - HM

get baseline characteristics

Step3: Check SNPs in the protein statistically diff - RZ

identify impact status

Moderate

affecting effectiveness

High

affects prot structure

Step2: Perform proteomics diff expression - RZ

Step1: Categorize groups - HM

Vit D def & normal lipid

463

Vit D def & Dyslepidimia def

114

Vit D normal & dyslepedimia

199

Vit D normal & normal lipid

851

lipid threshold

HDL

LDL

triglycerides

cholesterol

WORKFLOW 2: From 14k, we segregate samples into

previous work by others

3 dominant gene variants

CYP2R1

rs10741657

NADSYN1

rs12785878

rs2282679

~1223 samples

>12ng/ml, < 20 ng/ml

normal/sufficient

~1049 samples

>=20 ng/ml

~576 samples

how many of these 4205 samples have proteomics data

get the genetic variants profile

filter proteomics using "HDL associated proteins" ~ 100 types

low APO-X

high APO-X

proteomics expression analysis

find statistically sig protein expression

compared genetics w protein exp

MODIFIER

gtex

MODERATE

HIGH

match w n=270

compare the proteins

Subtopic

genetic variants that causes X to the proteins in previous studies

<12 ng/ml

WORKFLOW 1: get list of proteins enriched in vitD deficiency from our proteomics study (n=270)

find the genetic variants associated w them

indirect

non-coding region

coding but modifier

it regulates the expression of the protein

direct

coding region

moderate impact

it reduces the effectiveness of a protein

high impact

it affects protein structure formation

certain genes linking vitD defeciency with

some ppl have higher rate of deciciency compared to others

this means there might be genetic/inherited factors

Preliminary work

n=270

control

~90

case

~180

previously we look at

its molecular pathways associated with vitamin D deficiency and dyslipidemia

its anti-inflammatory potential

effects of vitamin D on HDL production

AIM

xxxxxx

Objectives

OBJ4

OBJ3

OBJ2

OBJ1

DATA

Metabolomics

Proteomics

#samples

orig 3000

inclusion/exclusion

exc = anyone with pregnancy

incl = do not suffer from chronic diseases

2000

sufficient

>20

655

insufficient

>=12,<20

821

deficient

<12

399

Genomics