ID

45677

Description

Principal Investigator: Daniel G. MacArthur, Broad Institute, Cambridge, MA, USA MeSH: Genetic Diseases, Inborn,Bardet-Biedl Syndrome,Blepharoptosis,Chorea,Ciliopathies,Coffin-Siris Syndrome,Congenital Abnormalities,Craniofacial Abnormalities,Developmental Disabilities,Growth Disorders,Hearing Loss, Sensorineural,Hypertelorism,Intellectual disability,Kidney Diseases,Lung Diseases, Interstitial,Macular Degeneration,Muscular Diseases,Neurodegenerative Diseases,Neurodevelopmental Disorders,Nervous System Malformations,Night Blindness,Retinal Degeneration,Retinitis Pigmentosa,Seizures,Spastic Paraplegia, Hereditary,Usher Syndromes https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001272 The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

Link

dbGaP study = phs001272

Keywords

Versions (1)
  1. 4/15/23 4/15/23 - Simon Heim
Copyright Holder

Daniel G. MacArthur, Broad Institute, Cambridge, MA, USA

Uploaded on

April 15, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001272 Broad Institute Center for Mendelian Genomics

English

Eligibility Criteria

6 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
*Prioritization Criteria:*
Description

*Prioritization Criteria:*

Data type

boolean

Alias
UMLS CUI [1,1]
C0549179
UMLS CUI [1,2]
C1261322
UMLS CUI [1,3]
C0243161
*Likely Mendelian cause:* The family has a highly penetrant severe and/or early onset phenotype, including those families with phenotypes matching a known but unsolved genetic condition. Families with multiple affected individuals, particularly cases that are consanguineous or large enough to obtain a significant LOD score through linkage, will be prioritized.
Description

*Likely Mendelian cause:* The family has a highly penetrant severe and/or early onset phenotype, including those families with phenotypes matching a known but unsolved genetic condition. Families with multiple affected individuals, particularly cases that are consanguineous or large enough to obtain a significant LOD score through linkage, will be prioritized.

Data type

boolean

Alias
UMLS CUI [1,1]
C0683231
UMLS CUI [1,2]
C0332148
UMLS CUI [1,3]
C0015576
UMLS CUI [1,4]
C0205250
UMLS CUI [1,5]
C0524899
UMLS CUI [1,6]
C0814120
UMLS CUI [1,7]
C0031437
UMLS CUI [2,1]
C5142998
UMLS CUI [2,2]
C0086282
UMLS CUI [2,3]
C0392760
UMLS CUI [2,4]
C0683568
UMLS CUI [2,5]
C4035618
UMLS CUI [2,6]
C0023956
UMLS CUI [2,7]
C0750502
UMLS CUI [2,8]
C0549179
*Pre-screened for known genetic causes:* For diseases with known genes, sample has undergone either targeted testing for the major genetic contributors to the phenotype, or exome sequencing.
Description

*Pre-screened for known genetic causes:* For diseases with known genes, sample has undergone either targeted testing for the major genetic contributors to the phenotype, or exome sequencing.

Data type

boolean

Alias
UMLS CUI [1,1]
C1527048
UMLS CUI [1,2]
C0220908
UMLS CUI [1,3]
C0728826
UMLS CUI [2,1]
C0012634
UMLS CUI [2,2]
C0205309
UMLS CUI [2,3]
C0017337
UMLS CUI [2,4]
C0370003
UMLS CUI [2,5]
C3863350
UMLS CUI [2,6]
C5575842
*Likely recessive or *de novo* dominant genetic cause:* Families with multiple affected siblings with unaffected parents, or with a known consanguineous relationship, will be favored over inherited dominant conditions. Probands with a strong suspicion of a *de novo* cause of disease (embryonic lethal/severe neonatal/pediatric disease) will also be prioritized if parental samples are available for trio analysis.
Description

*Likely recessive or *de novo* dominant genetic cause:* Families with multiple affected siblings with unaffected parents, or with a known consanguineous relationship, will be favored over inherited dominant conditions. Probands with a strong suspicion of a *de novo* cause of disease (embryonic lethal/severe neonatal/pediatric disease) will also be prioritized if parental samples are available for trio analysis.

Data type

boolean

Alias
UMLS CUI [1,1]
C0332148
UMLS CUI [1,2]
C0392755
UMLS CUI [1,3]
C4476722
UMLS CUI [1,4]
C5142998
UMLS CUI [1,5]
C0037047
UMLS CUI [1,6]
C0522476
UMLS CUI [1,7]
C2986417
UMLS CUI [1,8]
C0030551
UMLS CUI [1,9]
C0683568
UMLS CUI [1,10]
C1548789
UMLS CUI [2,1]
C0242114
UMLS CUI [2,2]
C1515568
UMLS CUI [2,3]
C1314792
UMLS CUI [2,4]
C0012634
UMLS CUI [2,5]
C0013936
UMLS CUI [2,6]
C2939425
UMLS CUI [2,7]
C1521725
UMLS CUI [2,8]
C0549179
UMLS CUI [2,9]
C0030551
UMLS CUI [2,10]
C0370003
UMLS CUI [2,11]
C0936012
*Multiple cases:* We will favor submissions for which there are multiple independent cases with the same rare phenotype.
Description

*Multiple cases:* We will favor submissions for which there are multiple independent cases with the same rare phenotype.

Data type

boolean

Alias
UMLS CUI [1,1]
C0868928
UMLS CUI [1,2]
C0439064
UMLS CUI [1,3]
C1548789
UMLS CUI [1,4]
C1515022
UMLS CUI [1,5]
C1853237
UMLS CUI [1,6]
C0445247
UMLS CUI [1,7]
C0522498
UMLS CUI [1,8]
C0031437
*Detailed clinical data and additional samples are available:* We will favor cases obtained by clinicians in active contact with the patient, for whom detailed medical records are available, and where obtaining additional clinical specimens and data are feasible.
Description

*Detailed clinical data and additional samples are available:* We will favor cases obtained by clinicians in active contact with the patient, for whom detailed medical records are available, and where obtaining additional clinical specimens and data are feasible.

Data type

boolean

Alias
UMLS CUI [1,1]
C0470187
UMLS CUI [1,2]
C1516606
UMLS CUI [1,3]
C1524062
UMLS CUI [2,1]
C1548789
UMLS CUI [2,2]
C1277697
UMLS CUI [2,3]
C0871685
UMLS CUI [2,4]
C0332158
UMLS CUI [2,5]
C0030705
UMLS CUI [2,6]
C0470187
UMLS CUI [2,7]
C0025102
UMLS CUI [2,8]
C1524062
UMLS CUI [2,9]
C2347026
UMLS CUI [2,10]
C0200345
UMLS CUI [2,11]
C3846158
*DNA and consent are available from multiple family members:* We will prioritize cases where DNA samples from additional family members, especially parents and affected relatives, are available for study.
Description

*DNA and consent are available from multiple family members:* We will prioritize cases where DNA samples from additional family members, especially parents and affected relatives, are available for study.

Data type

boolean

Alias
UMLS CUI [1,1]
C0470187
UMLS CUI [1,2]
C0012854
UMLS CUI [1,3]
C0021430
UMLS CUI [1,4]
C4316741
UMLS CUI [2,1]
C0549179
UMLS CUI [2,2]
C0470187
UMLS CUI [2,3]
C0012854
UMLS CUI [2,4]
C1524062
UMLS CUI [2,5]
C0086282
UMLS CUI [2,6]
C0030551
UMLS CUI [2,7]
C0080103
UMLS CUI [2,8]
C0522476
*Samples from a disease-relevant tissue are available for RNA-seq:* We will prioritize cases when patient samples from a tissue known to be impacted by the disease phenotype, or a relevant cell line (such as differentiated iPS cells), are available for transcriptome analysis.
Description

*Samples from a disease-relevant tissue are available for RNA-seq:* We will prioritize cases when patient samples from a tissue known to be impacted by the disease phenotype, or a relevant cell line (such as differentiated iPS cells), are available for transcriptome analysis.

Data type

boolean

Alias
UMLS CUI [1,1]
C2347026
UMLS CUI [1,2]
C0040300
UMLS CUI [1,3]
C0333125
UMLS CUI [1,4]
C0012634
UMLS CUI [1,5]
C0917793
UMLS CUI [2,1]
C0549179
UMLS CUI [2,2]
C2347026
UMLS CUI [2,3]
C0040300
UMLS CUI [2,4]
C0333125
UMLS CUI [2,5]
C4086242
UMLS CUI [2,6]
C0682523
UMLS CUI [2,7]
C5380756
*Resources are available for detailed follow-up analyses*: We will favor phenotypes for which there is clinical and biological/laboratory expertise available for the phenotype, and a clear path to targeted testing of candidate genes in other patients with similar phenotypes through local or international collaborations.
Description

*Resources are available for detailed follow-up analyses*: We will favor phenotypes for which there is clinical and biological/laboratory expertise available for the phenotype, and a clear path to targeted testing of candidate genes in other patients with similar phenotypes through local or international collaborations.

Data type

boolean

Alias
UMLS CUI [1,1]
C0470187
UMLS CUI [1,2]
C0035201
UMLS CUI [1,3]
C0016441
UMLS CUI [2,1]
C1548789
UMLS CUI [2,2]
C0031437
UMLS CUI [2,3]
C0870520
UMLS CUI [2,4]
C0205210
UMLS CUI [2,5]
C0205460
UMLS CUI [2,6]
C0039593
UMLS CUI [2,7]
C3846158
UMLS CUI [2,8]
C1332838
UMLS CUI [2,9]
C0205276
UMLS CUI [2,10]
C0392337
UMLS CUI [2,11]
C0021785
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Similar models

Eligibility Criteria

6 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
*Prioritization Criteria:*
Item
*Prioritization Criteria:*
boolean
C0549179 (UMLS CUI [1,1])
C1261322 (UMLS CUI [1,2])
C0243161 (UMLS CUI [1,3])
*Likely Mendelian cause:* The family has a highly penetrant severe and/or early onset phenotype, including those families with phenotypes matching a known but unsolved genetic condition. Families with multiple affected individuals, particularly cases that are consanguineous or large enough to obtain a significant LOD score through linkage, will be prioritized.
Item
*Likely Mendelian cause:* The family has a highly penetrant severe and/or early onset phenotype, including those families with phenotypes matching a known but unsolved genetic condition. Families with multiple affected individuals, particularly cases that are consanguineous or large enough to obtain a significant LOD score through linkage, will be prioritized.
boolean
C0683231 (UMLS CUI [1,1])
C0332148 (UMLS CUI [1,2])
C0015576 (UMLS CUI [1,3])
C0205250 (UMLS CUI [1,4])
C0524899 (UMLS CUI [1,5])
C0814120 (UMLS CUI [1,6])
C0031437 (UMLS CUI [1,7])
C5142998 (UMLS CUI [2,1])
C0086282 (UMLS CUI [2,2])
C0392760 (UMLS CUI [2,3])
C0683568 (UMLS CUI [2,4])
C4035618 (UMLS CUI [2,5])
C0023956 (UMLS CUI [2,6])
C0750502 (UMLS CUI [2,7])
C0549179 (UMLS CUI [2,8])
*Pre-screened for known genetic causes:* For diseases with known genes, sample has undergone either targeted testing for the major genetic contributors to the phenotype, or exome sequencing.
Item
*Pre-screened for known genetic causes:* For diseases with known genes, sample has undergone either targeted testing for the major genetic contributors to the phenotype, or exome sequencing.
boolean
C1527048 (UMLS CUI [1,1])
C0220908 (UMLS CUI [1,2])
C0728826 (UMLS CUI [1,3])
C0012634 (UMLS CUI [2,1])
C0205309 (UMLS CUI [2,2])
C0017337 (UMLS CUI [2,3])
C0370003 (UMLS CUI [2,4])
C3863350 (UMLS CUI [2,5])
C5575842 (UMLS CUI [2,6])
*Likely recessive or *de novo* dominant genetic cause:* Families with multiple affected siblings with unaffected parents, or with a known consanguineous relationship, will be favored over inherited dominant conditions. Probands with a strong suspicion of a *de novo* cause of disease (embryonic lethal/severe neonatal/pediatric disease) will also be prioritized if parental samples are available for trio analysis.
Item
*Likely recessive or *de novo* dominant genetic cause:* Families with multiple affected siblings with unaffected parents, or with a known consanguineous relationship, will be favored over inherited dominant conditions. Probands with a strong suspicion of a *de novo* cause of disease (embryonic lethal/severe neonatal/pediatric disease) will also be prioritized if parental samples are available for trio analysis.
boolean
C0332148 (UMLS CUI [1,1])
C0392755 (UMLS CUI [1,2])
C4476722 (UMLS CUI [1,3])
C5142998 (UMLS CUI [1,4])
C0037047 (UMLS CUI [1,5])
C0522476 (UMLS CUI [1,6])
C2986417 (UMLS CUI [1,7])
C0030551 (UMLS CUI [1,8])
C0683568 (UMLS CUI [1,9])
C1548789 (UMLS CUI [1,10])
C0242114 (UMLS CUI [2,1])
C1515568 (UMLS CUI [2,2])
C1314792 (UMLS CUI [2,3])
C0012634 (UMLS CUI [2,4])
C0013936 (UMLS CUI [2,5])
C2939425 (UMLS CUI [2,6])
C1521725 (UMLS CUI [2,7])
C0549179 (UMLS CUI [2,8])
C0030551 (UMLS CUI [2,9])
C0370003 (UMLS CUI [2,10])
C0936012 (UMLS CUI [2,11])
*Multiple cases:* We will favor submissions for which there are multiple independent cases with the same rare phenotype.
Item
*Multiple cases:* We will favor submissions for which there are multiple independent cases with the same rare phenotype.
boolean
C0868928 (UMLS CUI [1,1])
C0439064 (UMLS CUI [1,2])
C1548789 (UMLS CUI [1,3])
C1515022 (UMLS CUI [1,4])
C1853237 (UMLS CUI [1,5])
C0445247 (UMLS CUI [1,6])
C0522498 (UMLS CUI [1,7])
C0031437 (UMLS CUI [1,8])
*Detailed clinical data and additional samples are available:* We will favor cases obtained by clinicians in active contact with the patient, for whom detailed medical records are available, and where obtaining additional clinical specimens and data are feasible.
Item
*Detailed clinical data and additional samples are available:* We will favor cases obtained by clinicians in active contact with the patient, for whom detailed medical records are available, and where obtaining additional clinical specimens and data are feasible.
boolean
C0470187 (UMLS CUI [1,1])
C1516606 (UMLS CUI [1,2])
C1524062 (UMLS CUI [1,3])
C1548789 (UMLS CUI [2,1])
C1277697 (UMLS CUI [2,2])
C0871685 (UMLS CUI [2,3])
C0332158 (UMLS CUI [2,4])
C0030705 (UMLS CUI [2,5])
C0470187 (UMLS CUI [2,6])
C0025102 (UMLS CUI [2,7])
C1524062 (UMLS CUI [2,8])
C2347026 (UMLS CUI [2,9])
C0200345 (UMLS CUI [2,10])
C3846158 (UMLS CUI [2,11])
*DNA and consent are available from multiple family members:* We will prioritize cases where DNA samples from additional family members, especially parents and affected relatives, are available for study.
Item
*DNA and consent are available from multiple family members:* We will prioritize cases where DNA samples from additional family members, especially parents and affected relatives, are available for study.
boolean
C0470187 (UMLS CUI [1,1])
C0012854 (UMLS CUI [1,2])
C0021430 (UMLS CUI [1,3])
C4316741 (UMLS CUI [1,4])
C0549179 (UMLS CUI [2,1])
C0470187 (UMLS CUI [2,2])
C0012854 (UMLS CUI [2,3])
C1524062 (UMLS CUI [2,4])
C0086282 (UMLS CUI [2,5])
C0030551 (UMLS CUI [2,6])
C0080103 (UMLS CUI [2,7])
C0522476 (UMLS CUI [2,8])
*Samples from a disease-relevant tissue are available for RNA-seq:* We will prioritize cases when patient samples from a tissue known to be impacted by the disease phenotype, or a relevant cell line (such as differentiated iPS cells), are available for transcriptome analysis.
Item
*Samples from a disease-relevant tissue are available for RNA-seq:* We will prioritize cases when patient samples from a tissue known to be impacted by the disease phenotype, or a relevant cell line (such as differentiated iPS cells), are available for transcriptome analysis.
boolean
C2347026 (UMLS CUI [1,1])
C0040300 (UMLS CUI [1,2])
C0333125 (UMLS CUI [1,3])
C0012634 (UMLS CUI [1,4])
C0917793 (UMLS CUI [1,5])
C0549179 (UMLS CUI [2,1])
C2347026 (UMLS CUI [2,2])
C0040300 (UMLS CUI [2,3])
C0333125 (UMLS CUI [2,4])
C4086242 (UMLS CUI [2,5])
C0682523 (UMLS CUI [2,6])
C5380756 (UMLS CUI [2,7])
*Resources are available for detailed follow-up analyses*: We will favor phenotypes for which there is clinical and biological/laboratory expertise available for the phenotype, and a clear path to targeted testing of candidate genes in other patients with similar phenotypes through local or international collaborations.
Item
*Resources are available for detailed follow-up analyses*: We will favor phenotypes for which there is clinical and biological/laboratory expertise available for the phenotype, and a clear path to targeted testing of candidate genes in other patients with similar phenotypes through local or international collaborations.
boolean
C0470187 (UMLS CUI [1,1])
C0035201 (UMLS CUI [1,2])
C0016441 (UMLS CUI [1,3])
C1548789 (UMLS CUI [2,1])
C0031437 (UMLS CUI [2,2])
C0870520 (UMLS CUI [2,3])
C0205210 (UMLS CUI [2,4])
C0205460 (UMLS CUI [2,5])
C0039593 (UMLS CUI [2,6])
C3846158 (UMLS CUI [2,7])
C1332838 (UMLS CUI [2,8])
C0205276 (UMLS CUI [2,9])
C0392337 (UMLS CUI [2,10])
C0021785 (UMLS CUI [2,11])
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