News & Updates

AMP PD Release Notes – December 2020

Data Summary

Data Composition

Clinical Data

Single unified AMP PD cohort datasetParticipant records were compiled from seven cohorts and harmonized to form a single unified AMP PD cohort dataset. These records were then paired with RNA and WGS samples and excluded if matching sample data was not available, with the exception of 57  participants who appeared in multiple studies and whose duplicate WGS samples were excluded. Participants appearing in multiple studies and their corresponding samples are identified in release products so they may be traced to their associated clinical records from multiple studies. Growing from 4298 participants in our flagship launch on October 15, 2019, now 10,247 participants are represented in this v2 release by clinical records and at least one other data type.

Integrated Data

This release includes 2985 subjects with fully integrated clinical records, WGS samples, and RNA samples. For an additional 289 participants, this release includes RNA samples with corresponding clinical records where WGS is not available. There are similarly 6916 WGS samples with clinical records where RNA sample data is not available.

RNA Data

RNA sample data was sequenced and processed for BioFIND, PDBP, and PPMI cohort participants. The AMP PD v1 release featured 8356 RNA samples for 3225 Participants. In the latest v2 release, 105 RNA samples have been added, bringing the total participants in AMP PD with RNA samples to 3274. RNA samples were excluded from the v2 release when there was no corresponding clinical data. All RNA samples were vetted through a series of independent genomic QC checks and interdependent multi-modal QC checks.

WGS Data

DNA samples were sequenced and processed through the Broads GATK pipeline for BioFIND, HBS, LBD, LCC, PDBP, PPMI, and Steady PD cohort participants. WGS samples were excluded from the v2 release when there was no corresponding clinical data. All WGS samples were vetted through a series of independent genomic QC checks and interdependent multi-modal QC checks. In Q3 2020, AMP PD added TOPMed joint genotyped bcf data for 4047 AMP PD participants. In the v2 release dataset, all 9887 WGS samples are represented in the AMP PD Broad joint discovery vcf data,  which excludes 14 released samples that are flagged for further investigation. QC flags are identified and described in AMP PD release products for each WGS sample in the v2 release.

Composition by Cohort

BioFIND Data

Participants from the BioFIND cohort are represented in AMP PD clinical, RNA, and WGS data. Of 213 participants whose clinical records met AMP PD minimum clinical data criteria, 172 have corresponding WGS sample data (3 are represented by a linked WGS duplicate sample), 172 in the AMP PD joint genotyping dataset, 208 have corresponding RNA sample data, and 167 participants have corresponding samples in all three release data categories.

HBS Data

Participants from the Harvard Biomarkers Study (HBS) are represented in AMP PD clinical and WGS data. Of 1189 HBS participants whose clinical records met AMP PD minimum clinical data criteria, 1180 have corresponding WGS sample data (9 are represented by a linked WGS duplicate sample) and 1173 are represented in the AMP PD joint genotyping dataset.

PDBP Data

Participants from the Parkinson’s Disease Biomarkers Program (PDBP) are represented in AMP PD clinical, RNA, and WGS data. Of 1606 participants whose clinical records met AMP PD minimum clinical data criteria, 1505 have corresponding WGS sample data (7 are represented by a linked WGS duplicate sample), 1500 in the AMP PD joint genotyping dataset, 1484 have corresponding RNA sample data, and 1380 participants have corresponding samples in all three release data categories.

PPMI Data

Participants from the Parkinson’s Progression Markers Initiative (PPMI) are represented in AMP PD clinical, RNA, and WGS data. Of 1923 participants whose clinical records met AMP PD minimum clinical data criteria, 1775 have corresponding WGS sample data (6 are represented by a linked WGS duplicate sample), 1773 in the AMP PD joint genotyping dataset, 1582 have corresponding RNA sample data, and 1433 participants have corresponding samples in all three release data categories.

LBD Data

Participants from the Lewy Bodies Dementia (LBD) cohort are represented in AMP PD clinical and WGS data. Of 4586 HBS participants whose clinical records met AMP PD minimum clinical data criteria, 4579 have corresponding WGS sample data (7 are represented by a linked WGS duplicate sample) and 4579 are represented in the AMP PD joint genotyping dataset.

LCC Data

Participants from the LRRK2 Cohort Consortium (LCC) cohort are represented in AMP PD clinical and WGS data. Of 638 LCC participants whose clinical records met AMP PD minimum clinical data criteria, 599 have corresponding WGS sample data (39 are represented by a linked WGS duplicate sample) and 599 are represented in the AMP PD joint genotyping dataset.

Steady-PD

Participants from the Steady-PD cohort are represented in AMP PD clinical and WGS data. Of 92 Steady-PD cohort participants whose clinical records met AMP PD minimum clinical data criteria, 91 have corresponding WGS sample data (1 is represented by a linked WGS duplicate sample) and 91 are represented in the AMP PD joint genotyping dataset.

Google Cloud Storage

Participant Data Products

  • Table of all participants in all release data (n=10247)
  • Table of all participants with minimum diagnosis information
  • Table of all participant whole genome sequence samples in release data (n=9901)
  • Table of all participant (n=3274) transcriptomics samples (n=8461) in release data
  • Table of all participants who were included in more than one study and, therefore, appear in multiple clinical and transcriptomics samples (n=72).  For these genetically identical samples, a single WGS sample was selected with preference for the sample with higher mean coverage.
  • Harmonized clinical data
    • harmonized clinical data in 30 clinical forms as csv
    • harmonized clinical per-form dictionary files as csv

WGS Data Products

  • Table of all participant samples (n=9901) and processed file locations
  • Single sample processed data: CRAM, gVCF, and GATK processing metrics (n=9901)
  • Joint genotyping processed data: annotated variant vcf data (n=9887)
  • Plink files: aggregated plink bfiles from all processed vcf data (n=9887)
  • TOPMed joint genotyping processed data: annotated variant bcf data (n=4047)

RNA Data Products

  • Table of all RNA participant (n=3274) samples (n=8461) and processed file locations
  • Processed RNA sample data
    • picard metrics: Aggregated per-sample alignment summary metrics, insert size metrics, and rna seq metrics. (n=8461)
    • salmon quantification: Aggregated per-sample quantification estimates of the expression of transcripts and genes. Also available in matrix form. (n=8461)
    • star align-reads: Aggregated per-sample Log.final.out outputs. (n=8461)
    • feature counts: Aggregated per-sample featureCounts.tsv outputs. Also available in matrix form. (n=8461)
    • plink genomes: Pairwise comparison of participants' RNA and WGS samples to detect sample contaminations, swaps and relatedness. (n=8461)
    • multiqc reports: An html file containing visualizations from multiqc. Other multiqc artifacts are also available. (n=8461)
    • sequencing metrics: Metrics from the sequencing provider. (n=8356)

Google BigQuery

BigQuery Datasets

Participant Clinical Access BigQuery Dataset:

AMP PD Metadata Tables
amp_pd_participants
amp_pd_case_control
amp_pd_participant_wgs_duplicates
wgs_sample_inventory
rna_sample_inventory
 
Clinical Participant Tables
Demographics, PD_Medical_History, Enrollment, Caffeine_history, Family_History_PD, Smoking_and_alcohol_history, LBD_Cohort_Clinical_Data, LBD_Cohort_Path_Data
 
Clinical Assessments Tables
Epworth_Sleepiness_Scale, MDS_UPDRS_Part_I,MDS_UPDRS_Part_II, MDS_UPDRS_Part_III, MDS_UPDRS_Part_IV, MMSE, MOCA, Modified_Schwab___England_ADL, PDQ_39, REM_Sleep_Behavior_Disorder_Questionnaire_Mayo, REM_Sleep_Behavior_Disorder_Questionnaire_Stiasny_Kolster, UPDRS, UPSIT
 
Clinical Bio Tables
Biospecimen_analyses_CSF_abeta_tau_ptau,Biospecimen_analyses_CSF_beta_glucocerebrosidase, Biospecimen_analyses_other, Biospecimen_analyses_SomaLogic_plasma, DaTSCAN_SBR, DaTSCAN_visual_interpretation, MRI, DTI

Participant Tier 2 BigQuery Dataset:

AMP PD Metadata Tables
amp_pd_participant_mutations
Clinical Participant Tables
Clinically_Reported_Genetic_Status

WGS BigQuery Dataset:

WGS Joint Genotyping Tables (n=9887)
gatk_passing_variants
gatk_variant_calling_detail_metrics
WGS Single Sample Variant Metrics Tables (n=9901)
gatk_variant_calling_summary_metrics
WGS Single Sample Alignment Metrics Tables (n=9901)
raw_wgs_metrics, wgs_metrics, preBqsr_selfSM
WGS Sample Metadata Tables (n=9901)
wgs_samples
wgs_sample_flags

RNA BigQuery Dataset:  

RNA Sample Metadata Tables
rna_seq_samples
Picard  Tables
alignment_summary_metrics, insert_size_metrics, rna_seq_metrics
Salmon Tables
quantification_genes, quantification_transcripts
Star Tables
star_metrics
FeatureCounts Tables
feature_counts
Plink Tables
genome_check_HW_MAF
Sequencing Tables
rna_quality_metrics

V1 Release vs V2 Release Summary

AdditionsV2 Release

  • Added a new cohort:  LBD clinical and WGS samples
  • Added a new cohort:  LCC clinical and WGS samples
  • Added a new cohort:  Steady clinical and WGS samples
  • Added to HBS, PDBP, and PPMI cohorts:  clinical, WGS samples, and RNA samples
  • Added all QC passing samples to AMP PD joint genotyping
  • Added TOPMed Joint call bcf files
  • Added Plink 1.9 and 2.0 data

Changes

  • Modified WGS QC Process to resolve heterozygosity skew
  • V1 ReleaseFlagged v1_release samples that failed v2_release QC
  • Added Flags field to wgs_sample_inventory table
  • Added Flag Descriptions Table
  • Modified the mutations table, excluding SNCA variant H50Q (rs201106962) and changed the names on the names on the website to traditional numbering in lieu of amino acid change
  • Replaced and reformatted the duplicate_participants  table
  • Discontinued gatk_all_variants Table