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--- uk_biobank:phenotype_request [2016/04/08 10:22]
david
+++ uk_biobank:phenotype_request [2016/06/09 22:35] (current)
brooke_huibregtse
@@ Line 85: / Line 85: @@
 **The variable name, link to the variable, and Field ID for EACH variable, listed below:**
-. Brain MRI http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field 100
+. Brain MRI http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Category 100 - BULK
-. Death Registry http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100093 Field 100093
+. Death Registry http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100093 Category 100093
 . Job Coding http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=22601 Field 22601
@@ Line 97: / Line 97: @@
 **The research question you are planning to answer with the variables above:**
-After conducting a GWAS for left-handedness, we will use these variables to determine if the genetic correlates of left-handedness also affect other highly-correlated phenotypes such as schizophrenia, brain symmetry, and intelligence. We will also attempt to replicate previous hits and associations for left-handedness.
+After conducting a GWAS for left-handedness, we will use these variables to determine if the genetic correlates of left-handedness also affect other highly-correlated phenotypes. These phenotypes include schizophrenia diagnosis, so we are requesting ICD-10 diagnostic coding (Field 41202 and Field 41142), brain symmetry, function, and possible injury to parts of the brain (Category 100- Brain MRI), and creativity, which we will examine using Job Coding data (Field 22601) looking for people with jobs in artistic and/or creative fields. Similarly, we are requesting the death registry data (Category 100093), as previous research shows that left-handed people have a shorter life-span than right handed people. We will also attempt to replicate previous hits and associations for left-handedness.
@@ Line 108: / Line 108: @@
 ) Answered sexual history questions http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2129 Field ID 2129
-) Age first had sexual intercourse http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2139 Field ID 2139
+) Age first had sexual intercourse http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2139 Field ID 2139 -SENSITIVE
-) Lifetime number of sexual partners http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2149 Field ID 2149
+) Lifetime number of sexual partners http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2149 Field ID 2149 -SENSITIVE
-) Ever had same sex intercourse http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2159 Field ID 2159
+) Ever had same sex intercourse http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2159 Field ID 2159 -SENSITIVE
-) Lifetime number of same sex sexual partners http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=3669 Field ID 3669
+) Lifetime number of same sex sexual partners http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=3669 Field ID 3669 -SENSITIVE
+) Non-cancer illness code, self-reported http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=20002 Field ID 20002 (ALREADY HAVE)
+) Risk Taking  http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=2040 Field ID 2040 (ALREADY HAVE)
+) Alcohol Intake frequency http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=1558 Field ID 1558 (ALREADY HAVE)
 **The research question you are planning to answer with the variables above:**
-Some measures of sexual behavior, including age of sexual initiation, lifetime number of partners, and same-sex sexual relationships are risk factors for acquiring sexually transmitted infections, human immunodeficiency virus (HIV), and externalizing psychopathology such as drug use. Twin and family studies have demonstrated moderate heritabilites for a range of sexual behaviors, few studies have tested the extent to which these trait heritabilities are polygenic or tagged by common variants.  Genome wide analysis of these behaviors would inform theories regarding differing reproductive strategies, normative sexual behavior, and sexual behaviors that confer serious health risks.
+Some measures of sexual behavior, including age of sexual initiation and lifetime number of partners, are risk factors for acquiring sexually transmitted infections, human immunodeficiency virus (HIV), and externalizing psychopathology such as drug use. Same sex partnerships correspond to differential risk for infection, due to varying rates of transmission across types of sex acts as well as population differences in prevalence of infection. Twin and family studies have demonstrated moderate heritabilites for a range of sexual behaviors, few studies have tested the extent to which these trait heritabilities are polygenic or tagged by common variants.  Genome wide analysis of these behaviors would inform theories regarding differing reproductive strategies, normative sexual behavior, and sexual behaviors that confer serious health risks. Field ID 2149 (sensitive) is the major dependent variable of interest and is absolutely required. Field ID 3669 (sensitive) is required to test whether contextual factors (i.e. partner type, type of sex act) moderates risk. Field ID 2139 (sensitive) is highly correlated with number of partners, and is required to control for length of time participants have been sexually active. Predictors (risk taking and substance use) and outcomes (infections) are also requested for secondary analyses.
@@ Line 126: / Line 132: @@
 **The variable name, link to the variable, and Field ID for EACH variable, listed below:**
-. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026
+. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026 (ALREADY HAVE)
-. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100
+. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100 (INCLUDES BULK)
 . Cognitive function follow-up http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=116 Field 116
@@ Line 143: / Line 149: @@
 **The variable name, link to the variable, and Field ID for EACH variable, listed below:**
-. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026
+. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026 (ALREADY HAVE)
-. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100
+. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100 (INCLUDES BULK)
 . Cognitive function follow-up http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=116 Field 116
@@ Line 164: / Line 170: @@
 **The variable name, link to the variable, and Field ID for EACH variable, listed below:**
-. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026
+. Cognitive function http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100026 Field ID 100026 (ALREADY HAVE)
-. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100
+. Brain MRI  http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=100 Field ID 100 (INCLUDES BULK)
 . Cognitive function follow-up http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=116 Field 116
@@ Line 227: / Line 233: @@
 We will test whether the time to complete the touchscreen questionnaire can be used as an indicator of reading ability. If so, we will perform a genetic association analysis. Visual acuity variables are included as possible confounders. Field 393, which is sensitive, is absolutely required for this purpose. Completion time of the touchscreen questionnaire is likely to be dependent on the version of the touchscreen software used by a participant. We will need to segment our analysis using this variable.
+======= 10 =======
+**Your name:** Emma Johnson
+**The variable name, link to the variable, and Field ID for EACH variable, listed below:**
+. Home area population density http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=20118 Field 20118
+.  Length of time at current address http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=699 Field 699
+. Own or rent accommodation lived in http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=680 Field 680
+. Type of accommodation lived in http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=670 Field 670
+. Current employment status http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=6142 Field 6142
+. Time employed in main current job http://biobank.ctsu.ox.ac.uk/crystal/field.cgi?id=757 Field 757
+The research question you are planning to answer with the variables above:
+We are interested in doing a runs of homozygosity analysis in the UK Biobank data, assessing the relationship between these sociodemographic variables and autozygosity. Based on previous research and the ROH literature, we have reason to believe that various sociodemographic confounders can subtly bias the relationship between very distant inbreeding and psychiatric traits of interest, but many of our case-control datasets do not have these confounding variables measured, making it difficult to test the direction and strength of their influence. The variables listed above will allow us to test whether things like urban/rural location, education, employment, and other SES measures influence autozygosity and therefore could be influencing our ROH-psychiatric analyses.

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