eMERGE Network Supplemental Genotyping Project – Phenotype Description & Specifications
Height
Phenotype Description:
Version Date / June 14, 2010Contact / Jennifer A. Pacheco ()
Project Title / Genetic variation that predicts height.
Phenotype Description &Outline of Project /
- Exclude patients’ height measuresthat occur after any condition, medication, or procedure that affects height, at specified times, suchas only in childhood and/or adulthood (See Appendix fordetails such as timeframes, codes, & specific names):
- Diagnoses
- Genetic & Chromosomal abnormalities affecting height
- Adrenal, Pituitary, & Thyroid disorders
- Vertebral compression fractures
- Osteoporosis
- Other misc. disorders, history, etc.
- Medications used during childhood
- Growth Hormones (GH), inc. Receptor Antagonists & GHRH
- Steroids, i.e. androgens & anabolic steroids, Adrenal Steroid Inhibitors
- Labs & Procedures:
- Lab measuring GH which would indicate use of GH or potential issues w/ GH levels (result does not matter, as it is a rare lab at least in NU cohort) during childhood
- Lower limb (leg) amputations
- Collect all remaining height measurements by date and age
- Rule out height that is not between 130 & 250 cm (Gudbjartsson et.al, Nature Genetics, May 2008 v40(5) p.613.)
Sites Involved /Rough Estimate of Sample Size / Northwestern, Marshfield and Mayohave heightstored for >96% of subjects, while Group Health reports 76%, and Vanderbilt reports 64%, mostly stored as structured data. At Northwestern, after exclusion criteria ~81% of participants have at least 1 height measure that can be used for GWAS. Therefore, we estimate having 13,000 already genotyped individualsto study.
Scientific Relevance/ Rationale / GWAS for height have recently been reported, but these have, in general, been performed on lower densitychips (300,000-500,000 SNPs) and, similar to studies with lipids, most of the heritability of height is yet to be explained.
Desired variables (essential for analysis indicated by *) / *Basic demographic data: age, gender, race, ethnicity
*Height (cm)with date(s) and ages height collected
Source of height observation: self-report, measured (by someone other than patient), or unknown
Limitations/ Potential Obstacles/ Measurement Issues / Height in the EMR may either be measured by a clinician or self-reported, yet whether the height was self-reported or actually measured may not be noted. Also,height often declines (slightly) as we age. Deciding which height measure(s) to use is open for analysis and discussion.
Previous GWAS/ Genomic Literature on Phenotype / Reviewed in:
Visscher PM: Sizing up human height variation. Nat Genet 40:489-490, 2008.
APPENDIX
GH lab during childhood (females <= age 18, males <= age 21)(if lab ordered during childhood exclude patient altogether):
LOINC code 2963-7 :
“growth hormone” or “human growth hormone”
Medications during childhood (females <= age 18, males <= age 21)(if prescribed during childhood exclude patient altogether):
Generic name / Pharmaceutical class name / Source name / Source IDAminoglutethimide / Adrenal Steroid Inhibitors / RXNORM* / 677
trilostane / Adrenal Steroid Inhibitors / RXNORM* / 38668
Oxymetholone / Anabolic Steroids / RXNORM* / 7813
Oxandrolone / Anabolic Steroids / RXNORM* / 7779
Stanozolol / Anabolic Steroids / RXNORM* / 10032
Nandrolone / Anabolic Steroids / RXNORM* / 7244
testosterone topical / androgens and anabolic steroids / Multum / d04273
pegvisomant / Growth Hormone Receptor Antagonists / RXNORM* / 278739
Sermorelin / Growth Hormone Releasing Hormones (GHRH) / RXNORM* / 56188
somatrem / Growth Hormones / RXNORM* / 56570
Somatropin / Growth Hormones / RXNORM* / 61148
*Last time we looked there were some issues with our RxNorm mappings, so there may be some inaccurate mappings, refer to generic name where possible.
ICD-9 Dx affecting height:
Disorders in childhood (females <= age 18, males <= age 21) that would affect height (if occurred during childhood exclude patient altogether)
017.5Tuberculosis of thyroid gland
017.50Tuberculosis of thyroid gland, confirmation unspecified
017.51Tuberculosis of thyroid gland, bacteriological or histological examination not done
017.52Tuberculosis of thyroid gland, bacteriological or histological examination unknown (at present)
017.53Tuberculosis of thyroid gland, tubercle bacilli found (in sputum) by microscopy
017.54Tuberculosis of thyroid gland, tubercle bacilli not found (in sputum) by microscopy, but found by bacterial culture
017.55Tuberculosis of thyroid gland, tubercle bacilli not found by bacteriological examination, but tuberculosis confirmed histologically
017.56Tuberculosis of thyroid gland, tubercle bacilli not found by bacteriological or histological examination, but tuberculosis confirmed by other methods (inoculation of animals)
017.6Tuberculosis of adrenal glands
017.60Tuberculosis of adrenal glands, confirmation unspecified
017.61Tuberculosis of adrenal glands, bacteriological or histological examination not done
017.62Tuberculosis of adrenal glands, bacteriological or histological examination unknown (at present)
017.63Tuberculosis of adrenal glands, tubercle bacilli found (in sputum) by microscopy
017.64Tuberculosis of adrenal glands, tubercle bacilli not found (in sputum) by microscopy, but found by bacterial culture
017.65Tuberculosis of adrenal glands, tubercle bacilli not found by bacteriological examination, but tuberculosis confirmed histologically
017.66Tuberculosis of adrenal glands, tubercle bacilli not found by bacteriological or histological examination, but tuberculosis confirmed by other methods (inoculation of animals)
122.2Echinococcus granulosus infection of thyroid
193Malignant neoplasm of thyroid gland
194.0Malignant neoplasm of adrenal gland
194.1Malignant neoplasm of parathyroid gland
194.3Malignant neoplasm of pituitary gland and craniopharyngeal duct
198.7Secondary malignant neoplasm of adrenal gland
226Benign neoplasm of thyroid glands
227.0Benign neoplasm of adrenal gland
227.1Benign neoplasm of parathyroid gland
227.3Benign neoplasm of pituitary gland and craniopharyngeal duct (pouch)
237.0Neoplasm of uncertain behavior of pituitary gland and craniopharyngeal duct
237.2Neoplasm of uncertain behavior of adrenal gland
242.4Thyrotoxicosis from ectopic thyroid nodule
242.40Thyrotoxicosis from ectopic thyroid nodule without mention of thyrotoxic crisis or storm
242.41Thyrotoxicosis from ectopic thyroid nodule with mention of thyrotoxic crisis or storm
243Congenital hypothyroidism
244Acquired hypothyroidism
244.0Postsurgical hypothyroidism
244.1Other postablative hypothyroidism
244.2Iodine hypothyroidism
244.3Other iatrogenic hypothyroidism
244.8Other specified acquired hypothyroidism
244.9Unspecified hypothyroidism
245Thyroiditis
245.0Acute thyroiditis
245.1Subacute thyroiditis
245.2Chronic lymphocytic thyroiditis
245.3Chronic fibrous thyroiditis
245.4Iatrogenic thyroiditis
245.8Other and unspecified chronic thyroiditis
245.9Unspecified thyroiditis
246Other disorders of thyroid
246.2Cyst of thyroid
246.3Hemorrhage and infarction of thyroid
246.8Other specified disorders of thyroid
246.9Unspecified disorder of thyroid
252Disorders of parathyroid gland
252.0Hyperparathyroidism
252.00Hyperparathyroidism, unspecified
252.01Primary hyperparathyroidism
252.02Secondary hyperparathyroidism, non-renal
252.08Other hyperparathyroidism
252.1Hypoparathyroidism
252.8Other specified disorders of parathyroid gland
252.9Unspecified disorder of parathyroid gland
253Disorders of the pituitary gland and its hypothalamic control
253.1Other and unspecified anterior pituitary hyperfunction
253.4Other anterior pituitary disorders
253.7Iatrogenic pituitary disorders
253.8Other disorders of the pituitary and other syndromes of diencephalohypophyseal origin
253.9Unspecified disorder of the pituitary gland and its hypothalamic control
255Disorders of adrenal glands
255.3Other corticoadrenal overactivity
255.4Corticoadrenal insufficiency
255.5Other adrenal hypofunction
255.6Medulloadrenal hyperfunction
255.8Other specified disorders of adrenal glands
255.9Unspecified disorder of adrenal glands
263.2Arrested development following protein-calorie malnutrition
270.0Disturbances of amino-acid transport
277.5Mucopolysaccharidosis
377.51Disorders of optic chiasm associated with pituitary neoplasms and disorders
577.8Other specified disease of pancreas
588.0Renal osteodystrophy
588.81Secondary hyperparathyroidism (of renal origin)
628.1Female infertility of pituitary-hypothalamic origin
648.1Thyroid dysfunction complicating pregnancy, childbirth, or the puerperium
648.10Thyroid dysfunction of mother, complicating pregnancy, childbirth, or the puerperium, unspecified as to episode of care
648.11Thyroid dysfunction of mother, with delivery
648.12Thyroid dysfunction of mother, with delivery, with mention of postpartum complication
648.13Thyroid dysfunction, antepartum
648.14Thyroid dysfunction, postpartum
790.94Euthyroid sick syndrome
794.5Nonspecific abnormal results of thyroid function study
848.2Sprain and strain of thyroid region
868.01Adrenal gland injury without mention of open wound into cavity
868.11Adrenal gland injury, with open wound into cavity
874.2Open wound of thyroid gland, without mention of complication
874.3Open wound of thyroid gland, complicated
962.0Poisoning by adrenal cortical steroids
962.4Poisoning by anterior pituitary hormones
962.5Poisoning by posterior pituitary hormones
962.6Poisoning by parathyroid and parathyroid derivatives
962.7Poisoning by thyroid and thyroid derivatives
962.8Poisoning by antithyroid agents
E932.0Adrenal cortical steroids causing adverse effect in therapeutic use
E932.4Anterior pituitary hormones causing adverse effect in therapeutic use
E932.5Posterior pituitary hormones causing adverse effect in therapeutic use
E932.6Parathyroid and parathyroid derivatives causing adverse effect in therapeutic use
E932.7Thyroid and thyroid derivatives causing adverse effect in therapeutic use
E932.8Antithyroid agents causing adverse effect in therapeutic use
V10.87Personal history of malignant neoplasm of thyroid
V21.0Period of rapid growth in childhood
V54.02Encounter for lengthening/adjustment of growth rod
783.4Lack of expected normal physiological development in childhood
Diagnoses that may make height measurements inaccurate at any age, inc. Genetic & Chromosomal abnormalities affecting height (exclude height measurements that occur after these diagnoses):
897Traumatic amputation of leg(s) (complete) (partial)
897.0Traumatic amputation of leg(s) (complete) (partial), unilateral, below knee, without mention of complication
897.1Traumatic amputation of leg(s) (complete) (partial), unilateral, below knee, complicated
897.2Traumatic amputation of leg(s) (complete) (partial), unilateral, at or above knee, without mention of complication
897.3Traumatic amputation of leg(s) (complete) (partial), unilateral, at or above knee, complicated
897.4Traumatic amputation of leg(s) (complete) (partial), unilateral, level not specified, without mention of complication
897.5Traumatic amputation of leg(s) (complete) (partial), unilateral, level not specified, complicated
897.6Traumatic amputation of leg(s) (complete) (partial), bilateral (any level), without mention of complication
897.7Traumatic amputation of leg(s) (complete) (partial), bilateral (any level), complicated
V49.7Lower limb amputation status
V49.70Lower limb amputation, unspecified level
V49.73Lower limb amputation, foot
V49.74Lower limb amputation, ankle
V49.75Lower limb amputation, below knee
V49.76Lower limb amputation, above knee
V49.77Lower limb amputation, hip
733.0Osteoporosis
733.00Osteoporosis unspecified
733.01Senile Osteoporosis
733.02Idiopathic Osteoporosis
733.03Disuse Osteoporosis
733.09Other Osteoporosis
336.9Unspecified disease of spinal cord
733.13Pathologic fracture of vertebrae[JSA1]
805Fracture of vertebral column without mention of spinal cord injury
805.0Closed fracture of cervical vertebra without mention of spinal cord injury
805.00Closed fracture of cervical vertebra, unspecified level without mention of spinal cord injury
805.01Closed fracture of first cervical vertebra without mention of spinal cord injury
805.02Closed fracture of second cervical vertebra without mention of spinal cord injury
805.03Closed fracture of third cervical vertebra without mention of spinal cord injury
805.04Closed fracture of fourth cervical vertebra without mention of spinal cord injury
805.05Closed fracture of fifth cervical vertebra without mention of spinal cord injury
805.06Closed fracture of sixth cervical vertebra without mention of spinal cord injury
805.07Closed fracture of seventh cervical vertebra without mention of spinal cord injury
805.08Closed fracture of multiple cervical vertebrae without mention of spinal cord injury
805.1Open fracture of cervical vertebra without mention of spinal cord injury
805.10Open fracture of cervical vertebra, unspecified level without mention of spinal cord injury
805.11Open fracture of first cervical vertebra without mention of spinal cord injury
805.12Open fracture of second cervical vertebra without mention of spinal cord injury
805.13Open fracture of third cervical vertebra without mention of spinal cord injury
805.14Open fracture of fourth cervical vertebra without mention of spinal cord injury
805.15Open fracture of fifth cervical vertebra without mention of spinal cord injury
805.16Open fracture of sixth cervical vertebra without mention of spinal cord injury
805.17Open fracture of seventh cervical vertebra without mention of spinal cord injury
805.18Open fracture of multiple cervical vertebrae without mention of spinal cord injury
805.2Closed fracture of dorsal (thoracic) vertebra without mention of spinal cord injury
805.3Open fracture of dorsal (thoracic) vertebra without mention of spinal cord injury
805.4Closed fracture of lumbar vertebra without mention of spinal cord injury
805.5Open fracture of lumbar vertebra without mention of spinal cord injury
805.8Closed fracture of unspecified part of vertebral column without mention of spinal cord injury
805.9Open fracture of unspecified part of vertebral column without mention of spinal cord injury
806Fracture of vertebral column with spinal cord injury
806.0Closed fracture of cervical vertebra with spinal cord injury
806.1Open fracture of cervical vertebra with spinal cord injury
806.2Closed fracture of dorsal (thoracic) vertebra with spinal cord injury
806.3Open fracture of dorsal vertebra with spinal cord injury
806.8Closed fracture of unspecified vertebra with spinal cord injury
806.9Open fracture of unspecified vertebra with spinal cord injury
V54.17Aftercare for healing traumatic fracture of vertebrae
V54.27Aftercare for healing pathologic fracture of vertebrae
805.50FRACTURE OF VERTEBRAL COLUMN W/O MENTION OF SPINAL CORD INJURY;LUMBAR,OPEN;CERVICAL VERTEBRA,UNSPECIFIED LEVEL
253.3Pituitary dwarfism
259.4Dwarfism, not elsewhere classified
733.91Arrest of bone development or growth
756.4Chondrodystrophy
756.51Osteogenesis imperfecta
758.0Down's syndrome
758.6Gonadal dysgenesis
759.1Congenital anomalies of adrenal gland
759.81Prader-Willi syndrome
759.82Marfan's syndrome
759.89Other specified congenital anomalies, so described
781.91Loss of height
783.40Lack of normal physiological development, unspecified
783.43Short stature
Page 1 of 7
Last updated: 11/2/2018
[JSA1]Instead of these fracture diagnoses, can optionally use NLP to determine if vertebral compression fractures occurred, as no specific ICD-9 code for this type of fracture