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This example is currently in draft. |
Description of the context of the example for colleagues:
This example shows findings from an assessment of the unique pattern of allelic variation in genes of human leukocyte antigens (HLA), for purposes such as selecting cell, tissue and organ donors, diagnosing autoimmune diseases, determining the risk of adverse drug reactions, or to guide immunotherapies. An arbitrary identifier for the allele is represented in GFCOPYID. Patterns of HLA allele sequences are reported as short codes from a publicly available reference database that identifies the sequence in the database.
Patterns of HLA sequence are reported as short code from a publicly available reference database that corresponds to the sequence recorded in the database.
Assessment findings are reported as HLA allele names defined by a nomenclature from a publicly available registry.
Assessment findings are reported as HLA allele names constructed using publicly available a nomenclature.
In general, findings from assessments HLA allelic types may be reported in formats defined in publicly available reference databases. In this example,
In general, findings from assessments HLA allelic types may be reported defined codes in publicly available reference databases. In this example,
In general, findings from assessments HLA allelic types may be reported defined codes in publicly available reference databases. In this example,
Vendor is using a public reference. e
An assessment of the unique pattern of sequence variation of one to many loci associated with a normal or abnormal biological process.
Findings from assessments are reported a
Nomenclature for Factors of the HLA System
Nomenclature of HLA Alleles
Each HLA allele name has a unique number corresponding to up to four sets of digits separated by colons. The length of the allele designation is dependent on the sequence of the allele and that of its nearest relative. All alleles receive at least a four digit name, which corresponds to the first two sets of digits, longer names are only assigned when necessary.
HLA Nomenclature @ hla.alleles.org
https://bioinformatics.bethematchclinical.org/hla-resources/allele-codes/allele-code-lists/
An assessment of the unique pattern of sequence variation of one to many loci associated with a normal or abnormal biological process.
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Rows 1-9, 11, 15-16: | Show the characterization of the unique pattern of sequence variation for the allele of the HLA gene of interest represented in GFSYM. | Rows 10, 12-14: | Show attempted assessments for which results could not be generated due to sequence overlap with the detected DRB1 allele. |
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| Row # | STUDYID | DOMAIN | USUBJID | GFSEQ | GFREFID | GFTESTCD | GFTEST | GFTSTDTL | GFORRES | GFSYM | GFSYMTYP | GFCOPYID | GFSTAT | GFREASND | GFNAM | GFSPEC | GFMETHOD | VISITNUM | VISIT | VISITDY | GFDTC | GFDY | 1 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | A*02:TSXZ | HLA-A | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING | -1 | SCREENING | -1 | 9/16/2023 | -2 | 2 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | A*03:ABSAX | HLA-A | GENE WITH PROTEIN PRODUCT | 2 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 3 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | B*18:TXYF | HLA-B | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 4 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | B*38:01 | HLA-B | GENE WITH PROTEIN PRODUCT | 2 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 5 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | C*07:AAEPN | HLA-C | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 6 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | C*12:AAGWE | HLA-C | GENE WITH PROTEIN PRODUCT | 2 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 6 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DRB1*07:ACEUA | HLA-DRB1 | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 7 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DRB1*14:ABZZV | HLA-DRB1 | GENE WITH PROTEIN PRODUCT | 2 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 9 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DRB3*01:XX | HLA-DRB3 | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 10 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE |
| HLA-DRB3 | GENE WITH PROTEIN PRODUCT | 2 | NOT DONE | DRB3* | ACME Genomics | DNA | SANGER SEQUENCING |
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| 11 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DRB4*01:FVUU | HLA-DRB4 | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 12 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE |
| HLA-DRB4 | GENE WITH PROTEIN PRODUCT | 2 | NOT DONE | DRB4* | ACME Genomics | DNA | SANGER SEQUENCING |
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| 13 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE |
| HLA-DRB5 | GENE WITH PROTEIN PRODUCT | 1 | NOT DONE | DRB5* | ACME Genomics | DNA | SANGER SEQUENCING |
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| 14 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE |
| HLA-DRB5 | GENE WITH PROTEIN PRODUCT | 2 | NOT DONE | DRB5* | ACME Genomics | DNA | SANGER SEQUENCING |
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| 15 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DQB1*02:ACBXN | HLA-DQB1 | GENE WITH PROTEIN PRODUCT | 1 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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| 16 | Study-123 | GF | S123-001 | 1 | HGA4567 | VARPROF | Variant Profile | ALLELE TYPE | DQB1*05:ACEDB | HLA-DQB1 | GENE WITH PROTEIN PRODUCT | 2 |
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| ACME Genomics | DNA | SANGER SEQUENCING |
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