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Method Detail
Submitter Method Handle: PARC
Submitter Method ID: METHOD-E
Submitted method description:
FLUORESCENCE-BASED DNA SEQUENCING OF PCR AMPLICONS
DNA sequencing was performed on an ABI 3730XL DNA Analyzer.
All base calling for sequence chromatograms was done using Phred.
Polymorphism discovery was performed by alignment of sequencing chromatograms from multiple individuals using Phrap followed by analysis using the PolyPhred computer program to identify single nucleotide polymorphisms.
Program settings for PolyPhred (v. 4.0x) were:
-quality 25
-window 40
-rank 3
-scale1 1.00
-scale2 1.00
-tag genotype
-group .+
Genotypes for individual samples at each polymorphic site were assigned by PolyPhred.
All polymorphic sites and individual genotypes were confirmed by visual inspection.
Multiple strand coverage was available for greater than 40% of scanned sequence, with >99% confirmatio for called genotypes.
PARAMETER:
SEQUENCING_INSTRUMENT: ABI 3730XL DNA ANALYZER
BASE_CALLING_PROGRAM: PHRED
ASSEMBLY_PROGRAM: PHRAP
POLYMORPHISM_DETECTION_PROGRAM: POLYPHRED_4.0x
POLYPHRED_QUALITY: 25
POLYPHRED_SCALE1: 1.0
POLYPHRED_SCALE2: 1.0
POLYPHRED_GROUP: .+
POLYPHRED_RANK: RANK_3
GENOTYPES_ASSIGNED: POLYPHRED
MULTI_STRAND_COVERAGE: > 0.40

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
PARC Genotype AGT-AFRICAN-121503 119
PARC Genotype AGT-EUROPEAN-121503 119
PARC Genotype REN-EUROPEAN-011504 119
PARC Genotype REN-AFRICAN-011504 119
PARC Genotype LCAT-AFRICAN-051304 121
PARC Genotype LCAT-ROCHESTER-051304 121
PARC Genotype APOB-EUROPEAN-051304 121
PARC Genotype APOA1-ROCHESTER-051404 121
PARC Genotype PPARA-AFRICAN-051304 121
PARC Genotype PPARA-EUROPEAN-051304 121
PARC Genotype APOB-AFRICAN-051304 121
PARC Genotype PPARG-EUROPEAN-051304 121
PARC Genotype PPARG-AFRICAN-051304 121
PARC Genotype LDLR-AFRICAN-051304 121
PARC Genotype LDLR-EUROPEAN-051304 121
PARC Genotype APOA2-ROCHESTER-051404 121
PARC Genotype APOA4-ROCHESTER-051804 121
PARC Genotype APOC1-ROCHESTER-051804 121
PARC Genotype APOC2-AFRICAN-051804 121
PARC Genotype APOC2-ROCHESTER-051804 121
PARC Genotype APOC3-ROCHESTER-051804 121
PARC Genotype APOC4-AFRICAN-051804 121
PARC Genotype APOC4-ROCHESTER-051804 121
PARC Genotype HMGCR-AFRICAN-112204 123
PARC Genotype HMGCR-EUROPEAN-112204 123
PARC Frequency AGT-AFRICAN-121503 119
PARC Frequency AGT-EUROPEAN-121503 119
PARC Frequency REN-EUROPEAN-011504 119
PARC Frequency REN-AFRICAN-011504 119
PARC Frequency ACE-EUROPEAN-050604 121
PARC Frequency AGTR1-AFRICAN-050604 121
PARC Frequency AGTR1-EUROPEAN-050604 121
PARC Frequency AGTR2-AFRICAN-050604 121
PARC Frequency AGTR2-EUROPEAN-050604 121
PARC Frequency CETP-AFRICAN-050604 121
PARC Frequency HMGCR-AFRICAN-050604 121
PARC Frequency HMGCR-EUROPEAN-050604 121
PARC Frequency CETP-ROCHESTER-050704 121
PARC Frequency HMGCR-AFRICAN-112204 123
PARC Frequency HMGCR-EUROPEAN-112204 123
PARC Frequency APOA2-JACKSON-051707 127
PARC Frequency APOA4-JACKSON-051707 127
PARC Frequency APOA1-JACKSON-051707 127
PARC Frequency APOC1-JACKSON-051707 127
PARC Frequency APOC3-JACKSON-051707 127
PARC Assay AGT-AFRICAN-121503 119
PARC Assay AGT-EUROPEAN-121503 119
PARC Assay REN-EUROPEAN-011504 119
PARC Assay REN-AFRICAN-011504 119
PARC Assay ACE-EUROPEAN-050604 121
PARC Assay AGTR1-AFRICAN-050604 121
PARC Assay AGTR1-EUROPEAN-050604 121
PARC Assay AGTR2-AFRICAN-050604 121
PARC Assay AGTR2-EUROPEAN-050604 121
PARC Assay CETP-AFRICAN-050604 121
PARC Assay CETP-ROCHESTER-050704 121
PARC Assay LCAT-AFRICAN-051304 121
PARC Assay LCAT-ROCHESTER-051304 121
PARC Assay APOB-AFRICAN-051304 121
PARC Assay APOB-EUROPEAN-051304 121
PARC Assay PPARG-AFRICAN-051304 121
PARC Assay PPARG-EUROPEAN-051304 121
PARC Assay PPARA-AFRICAN-051304 121
PARC Assay PPARA-EUROPEAN-051304 121
PARC Assay LDLR-EUROPEAN-051304 121
PARC Assay LDLR-AFRICAN-051304 121
PARC Assay APOA1-ROCHESTER-051404 121
PARC Assay APOA2-ROCHESTER-051404 121
PARC Assay APOA4-ROCHESTER-051804 121
PARC Assay APOC1-ROCHESTER-051804 121
PARC Assay APOC2-AFRICAN-051804 121
PARC Assay APOC2-ROCHESTER-051804 121
PARC Assay APOC3-ROCHESTER-051804 121
PARC Assay APOC4-AFRICAN-051804 121
PARC Assay APOC4-ROCHESTER-051804 121
PARC Assay HMGCR-AFRICAN-112204 123
PARC Assay HMGCR-EUROPEAN-112204 123
PARC Assay APOA2-JACKSON-051707 127
PARC Assay APOA4-JACKSON-051707 127
PARC Assay APOA1-JACKSON-051707 127
PARC Assay APOC1-JACKSON-051707 127
PARC Assay APOC3-JACKSON-051707 127