ID

45602

Description

Principal Investigator: Jiyoung Ahn, PhD, Department of Population Health, NYU School of Medicine, NY, USA MeSH: Colonic Polyps,Adenomatous Polyps https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001381 Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma and the serrated polyp. This dataset was used to test the relationship of the gut microbiota to specific colorectal polyp types. We included samples from two independent study populations based at colonoscopy clinics: the Centers for Disease Control and Prevention (CDC) Study of In-home Tests for Colorectal Cancer (SIT), and the New York University (NYU) Human Microbiome and Colorectal Tumor study. Gut microbiota were assessed in 667 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples, of which 540 were included in our analysis. Participants were categorized as conventional adenoma cases, serrated polyp cases, or polyp-free controls. CA cases were further classified as proximal or distal and as non-advanced or advanced. Serrated polyp cases were further classified as hyperplastic polyp or sessile serrated adenoma. Our results show associations between gut microbiome composition and presence of conventional adenomas, including reduced diversity and alterations in taxon abundance.

Link

dbGaP-study=phs001381

Keywords

Versions (1)
  1. 2/15/23 2/15/23 - Chiara Middel
Copyright Holder

Jiyoung Ahn, PhD, Department of Population Health, NYU School of Medicine, NY, USA

Uploaded on

February 15, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001381 Gut Microbiome and Types of Colorectal Polyps

English

Subject ID, study, sex, race, age, familial polyposis, participant Crohn disease, ulcerative colitis, and gastrointestinal cancer, colonoscopy, anastomosis, carcinoid, inflammatory bowel disease, polyp(s), blood in stool or rectal bleeding, normal/non-polyp histology, sessile serrated adenoma(s), tubular adenoma(s), and tubulovillous adenoma of participants with or without colorectal polyps and involved in the "Gut Microbiome and Types of Colorectal Polyps" project.

5 forms  
pht006568
Description

pht006568

Alias
UMLS CUI [1,1]
C3846158
De-identified subject ID
Description

SUBJECT_ID

Data type

string

Alias
UMLS CUI [1,1]
C4684638
UMLS CUI [1,2]
C2348585
Gender of subject
Description

sex

Data type

text

Alias
UMLS CUI [1,1]
C0079399
Age of subject
Description

age

Data type

text

Measurement units
  • Years
Alias
UMLS CUI [1,1]
C0001779
Years
Body mass index of subject
Description

bmi

Data type

float

Measurement units
  • kg/m^2
Alias
UMLS CUI [1,1]
C1305855
kg/m^2
Race of subject
Description

race

Data type

text

Alias
UMLS CUI [1,1]
C0034510
Study in which the subject participated
Description

study

Data type

string

Alias
UMLS CUI [1,1]
C2348568
Presence of tubular adenoma(s) at colonoscopy
Description

ta

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0334292
UMLS CUI [1,3]
C0011008
UMLS CUI [1,4]
C0009378
Presence of tubulovillous adenoma(s) at colonoscopy
Description

tva

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C1333118
UMLS CUI [1,3]
C0011008
UMLS CUI [1,4]
C0009378
Presence of normal/non-polyp histology polyp(s) at colonoscopy
Description

normal

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0586627
UMLS CUI [1,3]
C0011008
UMLS CUI [1,4]
C0009378
Presence of sessile serrated adenoma(s) at colonoscopy
Description

ssa

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C2732618
UMLS CUI [1,3]
C0009378
Presence of sessile serrated adenoma(s) with dysplasia at colonoscopy
Description

ssa_dysplasia

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C2732618
UMLS CUI [1,3]
C0334044
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of hyperplastic polyp(s) at colonoscopy
Description

hyper

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0333983
UMLS CUI [1,3]
C0011008
UMLS CUI [1,4]
C0009378
Presence of polyp with unclassified histology at colonoscopy
Description

other_hist

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0205426
UMLS CUI [1,4]
C0019638
UMLS CUI [1,5]
C0011008
UMLS CUI [1,6]
C0009378
Antibiotic use in previous 30 days from stool collection
Description

antib

Data type

text

Alias
UMLS CUI [1,1]
C0338237
UMLS CUI [1,2]
C1547058
UMLS CUI [1,3]
C0015733
UMLS CUI [1,4]
C4064021
Presence of polyp(s) in cecum at colonoscopy
Description

cecum

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0032584
UMLS CUI [1,3]
C0007531
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in ascending colon at colonoscopy
Description

ascen

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0227375
UMLS CUI [1,3]
C0009376
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in hepatic flexure at colonoscopy
Description

hepflex

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0227385
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in transverse colon at colonoscopy
Description

transv

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0227386
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in splenic flexure at colonoscopy
Description

splenflex

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0227387
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in descending colon at colonoscopy
Description

desc

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0227389
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in sigmoid colon at colonoscopy
Description

sig

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C0227391
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Presence of polyp(s) in rectum at colonoscopy
Description

rec

Data type

text

Alias
UMLS CUI [1,1]
C3854307
UMLS CUI [1,2]
C0032584
UMLS CUI [1,3]
C0034896
UMLS CUI [1,4]
C0011008
UMLS CUI [1,5]
C0009378
Days from stool collection to colonoscopy
Description

time_days

Data type

text

Measurement units
  • Days
Alias
UMLS CUI [1,1]
C1265611
UMLS CUI [1,2]
C0439228
UMLS CUI [1,3]
C0430414
UMLS CUI [1,4]
C4064021
UMLS CUI [1,5]
C0009378
Days
Indication for colonoscopy was blood in stool or rectal bleeding
Description

ind_blood

Data type

text

Alias
UMLS CUI [1,1]
C3146298
UMLS CUI [1,2]
C0009378
UMLS CUI [1,3]
C0018932
UMLS CUI [1,4]
C0267596
Size of any tubular adenomas at colonoscopy
Description

tasize

Data type

text

Alias
UMLS CUI [1,1]
C0456389
UMLS CUI [1,2]
C0334292
UMLS CUI [1,3]
C0009378
Indication for colonoscopy was inflammatory bowel disease, colitis, or other related conditions
Description

ind_inf_disease

Data type

text

Alias
UMLS CUI [1,1]
C3146298
UMLS CUI [1,2]
C0009378
UMLS CUI [1,3]
C0021390
UMLS CUI [1,4]
C0009324
UMLS CUI [1,5]
C0205394
UMLS CUI [1,6]
C0012634
Indication for colonoscopy was personal history of gastrointestinal cancer
Description

ind_can

Data type

text

Alias
UMLS CUI [1,1]
C3146298
UMLS CUI [1,2]
C0009378
UMLS CUI [1,3]
C0262926
UMLS CUI [1,4]
C0685938
Self-reported ulcerative colitis
Description

dr_ulc

Data type

text

Alias
UMLS CUI [1,1]
C0681906
UMLS CUI [1,2]
C0009324
Self-reported Crohn disease
Description

dr_crohn

Data type

text

Alias
UMLS CUI [1,1]
C0681906
UMLS CUI [1,2]
C0010346
Additional finding at colonoscopy was inflammatory bowel disease
Description

add_ibd

Data type

text

Alias
UMLS CUI [1,1]
C1524062
UMLS CUI [1,2]
C0243095
UMLS CUI [1,3]
C0009378
UMLS CUI [1,4]
C0021390
Additional finding at colonoscopy was carcinoid tumor
Description

add_carc

Data type

text

Alias
UMLS CUI [1,1]
C1524062
UMLS CUI [1,2]
C0243095
UMLS CUI [1,3]
C0009378
UMLS CUI [1,4]
C0007095
Additional finding at colonoscopy was previous anastomosis
Description

add_astomosis

Data type

text

Alias
UMLS CUI [1,1]
C1524062
UMLS CUI [1,2]
C0243095
UMLS CUI [1,3]
C0009378
UMLS CUI [1,4]
C0205156
UMLS CUI [1,5]
C0332853
Self-reported familial polyposis
Description

dr_fpolyp

Data type

text

Alias
UMLS CUI [1,1]
C0681906
UMLS CUI [1,2]
C0241888
UMLS CUI [1,3]
C0032580
History of colorectal polyps other than study colonoscopy
Description

poly_his

Data type

text

Alias
UMLS CUI [1,1]
C0262926
UMLS CUI [1,2]
C0009376
UMLS CUI [1,3]
C4723751
UMLS CUI [1,4]
C0008976
UMLS CUI [1,5]
C0009378
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Similar models

Subject ID, study, sex, race, age, familial polyposis, participant Crohn disease, ulcerative colitis, and gastrointestinal cancer, colonoscopy, anastomosis, carcinoid, inflammatory bowel disease, polyp(s), blood in stool or rectal bleeding, normal/non-polyp histology, sessile serrated adenoma(s), tubular adenoma(s), and tubulovillous adenoma of participants with or without colorectal polyps and involved in the "Gut Microbiome and Types of Colorectal Polyps" project.

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht006568
C3846158 (UMLS CUI [1,1])
SUBJECT_ID
Item
De-identified subject ID
string
C4684638 (UMLS CUI [1,1])
C2348585 (UMLS CUI [1,2])
Item
Gender of subject
text
C0079399 (UMLS CUI [1,1])
sex
Code List
Gender of subject
CL Item
Female (0)
C0086287 (UMLS CUI [1,1])
CL Item
Male (1)
C0086582 (UMLS CUI [1,1])
age
Item
Age of subject
text
C0001779 (UMLS CUI [1,1])
bmi
Item
Body mass index of subject
float
C1305855 (UMLS CUI [1,1])
Item
Race of subject
text
C0034510 (UMLS CUI [1,1])
race
Code List
Race of subject
CL Item
White (0)
CL Item
Black (1)
CL Item
Other (2)
study
Item
Study in which the subject participated
string
C2348568 (UMLS CUI [1,1])
Item
Presence of tubular adenoma(s) at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0334292 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
C0009378 (UMLS CUI [1,4])
ta
Code List
Presence of tubular adenoma(s) at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of tubulovillous adenoma(s) at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C1333118 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
C0009378 (UMLS CUI [1,4])
tva
Code List
Presence of tubulovillous adenoma(s) at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of normal/non-polyp histology polyp(s) at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0586627 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
C0009378 (UMLS CUI [1,4])
normal
Code List
Presence of normal/non-polyp histology polyp(s) at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of sessile serrated adenoma(s) at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C2732618 (UMLS CUI [1,2])
C0009378 (UMLS CUI [1,3])
ssa
Code List
Presence of sessile serrated adenoma(s) at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of sessile serrated adenoma(s) with dysplasia at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C2732618 (UMLS CUI [1,2])
C0334044 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
ssa_dysplasia
Code List
Presence of sessile serrated adenoma(s) with dysplasia at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of hyperplastic polyp(s) at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0333983 (UMLS CUI [1,2])
C0011008 (UMLS CUI [1,3])
C0009378 (UMLS CUI [1,4])
hyper
Code List
Presence of hyperplastic polyp(s) at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Presence of polyp with unclassified histology at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0205426 (UMLS CUI [1,3])
C0019638 (UMLS CUI [1,4])
C0011008 (UMLS CUI [1,5])
C0009378 (UMLS CUI [1,6])
other_hist
Code List
Presence of polyp with unclassified histology at colonoscopy
CL Item
None (0)
CL Item
One or more (1)
Item
Antibiotic use in previous 30 days from stool collection
text
C0338237 (UMLS CUI [1,1])
C1547058 (UMLS CUI [1,2])
C0015733 (UMLS CUI [1,3])
C4064021 (UMLS CUI [1,4])
antib
Code List
Antibiotic use in previous 30 days from stool collection
CL Item
No (0)
CL Item
Yes (1)
cecum
Item
Presence of polyp(s) in cecum at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0032584 (UMLS CUI [1,2])
C0007531 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
ascen
Item
Presence of polyp(s) in ascending colon at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0227375 (UMLS CUI [1,2])
C0009376 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
hepflex
Item
Presence of polyp(s) in hepatic flexure at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0227385 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
transv
Item
Presence of polyp(s) in transverse colon at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0227386 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
splenflex
Item
Presence of polyp(s) in splenic flexure at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0227387 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
desc
Item
Presence of polyp(s) in descending colon at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0227389 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
sig
Item
Presence of polyp(s) in sigmoid colon at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C0227391 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
rec
Item
Presence of polyp(s) in rectum at colonoscopy
text
C3854307 (UMLS CUI [1,1])
C0032584 (UMLS CUI [1,2])
C0034896 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
time_days
Item
Days from stool collection to colonoscopy
text
C1265611 (UMLS CUI [1,1])
C0439228 (UMLS CUI [1,2])
C0430414 (UMLS CUI [1,3])
C4064021 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
Item
Indication for colonoscopy was blood in stool or rectal bleeding
text
C3146298 (UMLS CUI [1,1])
C0009378 (UMLS CUI [1,2])
C0018932 (UMLS CUI [1,3])
C0267596 (UMLS CUI [1,4])
ind_blood
Code List
Indication for colonoscopy was blood in stool or rectal bleeding
CL Item
No (0)
CL Item
Yes (1)
Item
Size of any tubular adenomas at colonoscopy
text
C0456389 (UMLS CUI [1,1])
C0334292 (UMLS CUI [1,2])
C0009378 (UMLS CUI [1,3])
tasize
Code List
Size of any tubular adenomas at colonoscopy
CL Item
None of this type (1)
CL Item
Some, all less than 10 mm (2)
CL Item
Some greater than or equal to 10 mm (3)
Item
Indication for colonoscopy was inflammatory bowel disease, colitis, or other related conditions
text
C3146298 (UMLS CUI [1,1])
C0009378 (UMLS CUI [1,2])
C0021390 (UMLS CUI [1,3])
C0009324 (UMLS CUI [1,4])
C0205394 (UMLS CUI [1,5])
C0012634 (UMLS CUI [1,6])
ind_inf_disease
Code List
Indication for colonoscopy was inflammatory bowel disease, colitis, or other related conditions
CL Item
No (0)
CL Item
Yes (1)
Item
Indication for colonoscopy was personal history of gastrointestinal cancer
text
C3146298 (UMLS CUI [1,1])
C0009378 (UMLS CUI [1,2])
C0262926 (UMLS CUI [1,3])
C0685938 (UMLS CUI [1,4])
ind_can
Code List
Indication for colonoscopy was personal history of gastrointestinal cancer
CL Item
No (0)
CL Item
Yes (1)
Item
Self-reported ulcerative colitis
text
C0681906 (UMLS CUI [1,1])
C0009324 (UMLS CUI [1,2])
dr_ulc
Code List
Self-reported ulcerative colitis
CL Item
No (0)
CL Item
Yes (1)
Item
Self-reported Crohn disease
text
C0681906 (UMLS CUI [1,1])
C0010346 (UMLS CUI [1,2])
dr_crohn
Code List
Self-reported Crohn disease
CL Item
No (0)
CL Item
Yes (1)
Item
Additional finding at colonoscopy was inflammatory bowel disease
text
C1524062 (UMLS CUI [1,1])
C0243095 (UMLS CUI [1,2])
C0009378 (UMLS CUI [1,3])
C0021390 (UMLS CUI [1,4])
add_ibd
Code List
Additional finding at colonoscopy was inflammatory bowel disease
CL Item
No (0)
CL Item
Yes (1)
Item
Additional finding at colonoscopy was carcinoid tumor
text
C1524062 (UMLS CUI [1,1])
C0243095 (UMLS CUI [1,2])
C0009378 (UMLS CUI [1,3])
C0007095 (UMLS CUI [1,4])
add_carc
Code List
Additional finding at colonoscopy was carcinoid tumor
CL Item
No (0)
CL Item
Yes (1)
Item
Additional finding at colonoscopy was previous anastomosis
text
C1524062 (UMLS CUI [1,1])
C0243095 (UMLS CUI [1,2])
C0009378 (UMLS CUI [1,3])
C0205156 (UMLS CUI [1,4])
C0332853 (UMLS CUI [1,5])
add_astomosis
Code List
Additional finding at colonoscopy was previous anastomosis
CL Item
No (0)
CL Item
Yes (1)
Item
Self-reported familial polyposis
text
C0681906 (UMLS CUI [1,1])
C0241888 (UMLS CUI [1,2])
C0032580 (UMLS CUI [1,3])
dr_fpolyp
Code List
Self-reported familial polyposis
CL Item
No (0)
CL Item
Yes (1)
Item
History of colorectal polyps other than study colonoscopy
text
C0262926 (UMLS CUI [1,1])
C0009376 (UMLS CUI [1,2])
C4723751 (UMLS CUI [1,3])
C0008976 (UMLS CUI [1,4])
C0009378 (UMLS CUI [1,5])
poly_his
Code List
History of colorectal polyps other than study colonoscopy
CL Item
No (0)
CL Item
Yes (1)
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