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Family Data Examples from source (original) data submissions #195

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lopierra opened this issue Jun 17, 2024 · 2 comments
Open

Family Data Examples from source (original) data submissions #195

lopierra opened this issue Jun 17, 2024 · 2 comments
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@lopierra
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HTP:

  • They provided their own Family Type enums and Proband designations
  • For some reason the Proband ID is listed under "OtherFamilyMemberID" - this is not as intended; this col was meant for like grandparents, etc.
  • F0084 and F0088 are examples of families with two Probands
  • There are also larger control-only families, e.g. F0023 - these families don't have Probands

X01-Hakonarson:

  • I'm not sure if there are any 2-proband families, but there are some more different relationships in this dataset
  • e.g. KFDS0563717437 has grandparents, mother, and proband
  • Note that many of the participants have 2 samples (DNA + RNA) so they will have 2 rows of data

DS-Connect IHQ (initial health questionnaire):

  • They did not designate Probands (all of the participants in the study have DS)
  • If there are 2 children enrolled in the same family, the Patient ID of the first one to enroll becomes the "Parent ID" for the 2nd sibling

DS-Sleep:

  • They designated probands and family relationships
  • There is one family with 2 probands (twins) - 113

TEAM-DS:

  • All of their participants have DS
  • They did not provide any proband or family information, but when asked, they informed me that there were 2 sibling pairs (101061/101062 and 101088/101089)

ABC-DS:

  • They did not provide proband designations or family info, but they provided a separate mapping of participants (col B, ABCDS_ID_DS) and their matched sibling controls (col A, ABCDS_ID_SC). Most participants did not have sibling controls.
@lopierra lopierra pinned this issue Jun 18, 2024
@lopierra
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We should also consider improving the enums for Family Type to be more descriptive, which would be especially helpful to summarize if we plan to provide a lot more detailed relationship data.

Currently we have:

  • Control-only
  • Proband-only
  • Duo (1 parent + 1 child)
  • Trio (2 parents + 1 child)
  • Trio+ (2 parents + >1 children + other relatives)
  • Other (Siblings only, 1 parent + >1 children, grandparents, etc.)

HTP has more descriptive Family Types for both T21 and D21 families - maybe something like what they're using?

  • D21 Only
  • D21-Multiple Sibs
  • D21-Parent Duo
  • D21-Parent-Multiple Sibs
  • D21-Parents Trio
  • D21-Parents-Multiple Sibs
  • D21-Sib Duo
  • T21 Only
  • T21-Multiple Sibs
  • T21-Other Trio
  • T21-Parent Duo
  • T21-Parent-Multiple Sibs
  • T21-Parents Trio
  • T21-Parent-Sib Trio
  • T21-Parents-Multiple Sibs
  • T21-Parents-Sib Quad
  • T21-Sib Duo

@lopierra lopierra assigned lopierra and unassigned mbrush Dec 20, 2024
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