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Add sanitized Phase-0 research archive under docs/research

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Research notes R1-R4, documentation-study files A-E (source of the
functional spec's `src:` tags) and PGx coverage CSVs, rewritten to use
neutral naming and current project decisions (plan §2).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-27 16:27:34 +01:00
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docs/research/pgx_masked_variants.csv
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product,manifest,gene,variant_ids
GDA-ePGx,GDA_PGx-8v1-0_20042614_G,CYP1A2,ilmnseq_rs35694136_ilmnfwd;ilmnseq_rs35694136_ilmnfwd_ilmndup1;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup3;ilmnseq_rs35694136_ilmnfwd_ilmndup4;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;ilmnseq_rs35694136_ilmnfwd_ilmndup7
GDA-ePGx,GDA_PGx-8v1-0_20042614_G,CYP2D6,ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_IlmnRep;ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_ilmndup1;ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_ilmndup3;ilmnseq_rs72549352_ilmnrev_F2BTindel_ilmndup1;ilmnseq_rs72549352_ilmnrev_F2BTindel_ilmndup3
GDA-ePGx,GDA_PGx-8v1-0_20042614_G,CYP4F2,ilmnseq_rs4020346_ilmnfwd
GDA-ePGx,GDA_PGx-8v1-0_20042614_G,UGT1A1,ilmnseq_rs8175347_ilmnfwd_F2BTindel;ilmnseq_rs8175347_ilmnfwd_F2BTindel_ilmndup1;ilmnseq_rs8175347_ilmnrev;ilmnseq_rs8175347_ilmnrev_ilmndup1;ilmnseq_rs8175347_ilmnrev_ilmndup2;ilmnseq_rs8175347_ilmnrev_ilmndup3
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP1A2,IlmnSeq_rs35694136_IlmnFWD;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup3;ilmnseq_rs35694136_ilmnfwd_ilmndup4;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;ilmnseq_rs35694136_ilmnfwd_ilmndup7
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2C19,"IlmnSeq_rs367543002,ilmnseq_rs367543002_ilmnfwd,ilmnseq_rs367543002_ilmnfwd_ilmndup1,ilmnseq_rs367543002_ilmnrev_deg3a1b0_ilmndup1,rs367543002"
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2C19,"ilmnseq_rs17882687_ilmnfwd_ilmndup2,ilmnseq_rs17882687_ilmnrev,ilmnseq_rs17882687_ilmnrev_ilmndup1,ilmnseq_rs17882687_ilmnrev_ilmndup2"
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2C19,"IlmnSeq_rs113934938,ilmnseq_rs113934938_ilmnfwd,ilmnseq_rs113934938_ilmnfwd_ilmndup1,ilmnseq_rs113934938_ilmnfwd_ilmndup2,rs113934938"
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2C9,"10:96701973,ilmnseq_rs774607211_ilmnfwd_ilmndup1,ilmnseq_rs774607211_ilmnfwd_ilmndup2"
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2D6,ilmnseq_rs1135836_ilmnrev_deg3a3b0
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP2D6,"PGX_IlmnSeq_rs769157652_BEST,ilmnseq_rs769157652_ilmnrev_F2BT,ilmnseq_rs769157652_ilmnrev_deg3a1b0"
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,CYP4F2,ilmnseq_rs4020346_ilmnfwd
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,OPRM1,ilmnseq_rs9384179.1_F2BT
GSAv4-ePGx,GSA-PGx-48v4-0_20079540_E,UGT1A1,ilmnseq_rs8175347.2_ilmnrev_F2BTindel_cei_ilmndup31
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,COMT,ilmnseq_rs7287550_ilmnfwd_F2BT
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP1A2,IlmnSeq_rs35694136;IlmnSeq_rs35694136_IlmnFWD;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;rs35694136
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2C19,ilmnseq_rs367543002_ilmnfwd
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2C19,"ilmnseq_rs17882687_ilmnfwd_ilmndup2,ilmnseq_rs17882687_ilmnrev_ilmndup1"
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2C19,"IlmnSeq_rs113934938,ilmnseq_rs113934938_ilmnfwd,ilmnseq_rs113934938_ilmnfwd_ilmndup1,ilmnseq_rs113934938_ilmnfwd_ilmndup2,rs113934938"
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2C9,"ilmnseq_rs774607211_ilmnrev,ilmnseq_rs774607211_ilmnrev_ilmndup2"
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2D6,ilmnseq_rs2004511_dup1
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP2D6,"PGX_IlmnSeq_rs769157652_BEST,ilmnseq_rs769157652_ilmnrev,ilmnseq_rs769157652_ilmnrev_deg3a1b0,ilmnseq_rs769157652_ilmnrev_deg3a1b0_ilmndup1,ilmnseq_rs769157652_ilmnrev_ilmndup1,seq-rs61737947"
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,CYP4F2,ilmnseq_rs4020346_ilmnfwd
GCRA-ePGx,GCRA-PGx-24v1-0_20084467_C,OPRM1,ilmnseq_rs9384179.1_F2BT
1 product manifest gene variant_ids
2 GDA-ePGx GDA_PGx-8v1-0_20042614_G CYP1A2 ilmnseq_rs35694136_ilmnfwd;ilmnseq_rs35694136_ilmnfwd_ilmndup1;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup3;ilmnseq_rs35694136_ilmnfwd_ilmndup4;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;ilmnseq_rs35694136_ilmnfwd_ilmndup7
3 GDA-ePGx GDA_PGx-8v1-0_20042614_G CYP2D6 ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_IlmnRep;ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_ilmndup1;ilmnseq_rs72549352_ilmnrev_F2BTindel_deg3a3b3_ilmndup3;ilmnseq_rs72549352_ilmnrev_F2BTindel_ilmndup1;ilmnseq_rs72549352_ilmnrev_F2BTindel_ilmndup3
4 GDA-ePGx GDA_PGx-8v1-0_20042614_G CYP4F2 ilmnseq_rs4020346_ilmnfwd
5 GDA-ePGx GDA_PGx-8v1-0_20042614_G UGT1A1 ilmnseq_rs8175347_ilmnfwd_F2BTindel;ilmnseq_rs8175347_ilmnfwd_F2BTindel_ilmndup1;ilmnseq_rs8175347_ilmnrev;ilmnseq_rs8175347_ilmnrev_ilmndup1;ilmnseq_rs8175347_ilmnrev_ilmndup2;ilmnseq_rs8175347_ilmnrev_ilmndup3
6 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP1A2 IlmnSeq_rs35694136_IlmnFWD;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup3;ilmnseq_rs35694136_ilmnfwd_ilmndup4;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;ilmnseq_rs35694136_ilmnfwd_ilmndup7
7 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2C19 IlmnSeq_rs367543002,ilmnseq_rs367543002_ilmnfwd,ilmnseq_rs367543002_ilmnfwd_ilmndup1,ilmnseq_rs367543002_ilmnrev_deg3a1b0_ilmndup1,rs367543002
8 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2C19 ilmnseq_rs17882687_ilmnfwd_ilmndup2,ilmnseq_rs17882687_ilmnrev,ilmnseq_rs17882687_ilmnrev_ilmndup1,ilmnseq_rs17882687_ilmnrev_ilmndup2
9 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2C19 IlmnSeq_rs113934938,ilmnseq_rs113934938_ilmnfwd,ilmnseq_rs113934938_ilmnfwd_ilmndup1,ilmnseq_rs113934938_ilmnfwd_ilmndup2,rs113934938
10 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2C9 10:96701973,ilmnseq_rs774607211_ilmnfwd_ilmndup1,ilmnseq_rs774607211_ilmnfwd_ilmndup2
11 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2D6 ilmnseq_rs1135836_ilmnrev_deg3a3b0
12 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP2D6 PGX_IlmnSeq_rs769157652_BEST,ilmnseq_rs769157652_ilmnrev_F2BT,ilmnseq_rs769157652_ilmnrev_deg3a1b0
13 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E CYP4F2 ilmnseq_rs4020346_ilmnfwd
14 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E OPRM1 ilmnseq_rs9384179.1_F2BT
15 GSAv4-ePGx GSA-PGx-48v4-0_20079540_E UGT1A1 ilmnseq_rs8175347.2_ilmnrev_F2BTindel_cei_ilmndup31
16 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C COMT ilmnseq_rs7287550_ilmnfwd_F2BT
17 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP1A2 IlmnSeq_rs35694136;IlmnSeq_rs35694136_IlmnFWD;ilmnseq_rs35694136_ilmnfwd_ilmndup2;ilmnseq_rs35694136_ilmnfwd_ilmndup5;ilmnseq_rs35694136_ilmnfwd_ilmndup6;rs35694136
18 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2C19 ilmnseq_rs367543002_ilmnfwd
19 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2C19 ilmnseq_rs17882687_ilmnfwd_ilmndup2,ilmnseq_rs17882687_ilmnrev_ilmndup1
20 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2C19 IlmnSeq_rs113934938,ilmnseq_rs113934938_ilmnfwd,ilmnseq_rs113934938_ilmnfwd_ilmndup1,ilmnseq_rs113934938_ilmnfwd_ilmndup2,rs113934938
21 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2C9 ilmnseq_rs774607211_ilmnrev,ilmnseq_rs774607211_ilmnrev_ilmndup2
22 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2D6 ilmnseq_rs2004511_dup1
23 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP2D6 PGX_IlmnSeq_rs769157652_BEST,ilmnseq_rs769157652_ilmnrev,ilmnseq_rs769157652_ilmnrev_deg3a1b0,ilmnseq_rs769157652_ilmnrev_deg3a1b0_ilmndup1,ilmnseq_rs769157652_ilmnrev_ilmndup1,seq-rs61737947
24 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C CYP4F2 ilmnseq_rs4020346_ilmnfwd
25 GCRA-ePGx GCRA-PGx-24v1-0_20084467_C OPRM1 ilmnseq_rs9384179.1_F2BT