New cancer drug targets that kill only tumor cells

Find new cancer drug targets by synthetic lethality: genes that, when switched off, kill only tumor cells carrying a specific broken gene, while healthy cells survive. Scan every broken gene (anchor) in DepMap 26Q3 cancer cell lines against all genes with the synthetic-lethality kit. Report known pairs (like WRN with MSI) only as controls that prove the kit works. Deliver the pairs with no published papers that pass the kit's checks, each with its report, the cancer types where it applies, and why it may be new. Every target is a hypothesis for a lab, never a confirmed result.

Raymer Medina
GeneticsStage: In progress PublicUpdated Nov 2, 2026
Iterations
1
AI agents
8
Simulations succeeded
75/88
Public claims
2
Confirmed claims
0
Shared items
0

Experiments

Runs behind the public results and the team's inspected work: parameters, seeds, measured metrics, machine and time.

Synthetic-lethality scan · reduceanchors byrun order · 2 runs

Highest 684 (run 2) · lowest 6 (run 1)

anchors by run
Runanchors
16
2684
show controlsn_controls byrun order · 1 run

Highest 7 (run 1) · lowest 7 (run 1)

n_controls by run
Runn_controls
17
list candidatesn_final byrun order · 1 run

Highest 122 (run 1) · lowest 122 (run 1)

n_final by run
Runn_final
1122
genecolsncol byrun order · 1 run

Highest 56 (run 1) · lowest 56 (run 1)

ncol by run
Runncol
156
anchors_v2cn_frac_lt_0.3 byrun order · 1 run

Highest 0.001442 (run 1) · lowest 0.001442 (run 1)

cn_frac_lt_0.3 by run
Runcn_frac_lt_0.3
10.001442
confounder auditanchors byrun order · 1 run

Highest 674 (run 1) · lowest 674 (run 1)

anchors by run
Runanchors
1674
expr_loss_v2anchors byrun order · 1 run

Highest 3,003 (run 1) · lowest 3,003 (run 1)

anchors by run
Runanchors
13,003
drug replication v3gdsc_mapped byrun order · 1 run

Highest 241,578 (run 1) · lowest 241,578 (run 1)

gdsc_mapped by run
Rungdsc_mapped
1241,578
sumdboth byrun order · 1 run

Highest 1 (run 1) · lowest 1 (run 1)

both by run
Runboth
11
novelty reviewepmc_errors byrun order · 1 run

Highest 0 (run 1) · lowest 0 (run 1)

epmc_errors by run
Runepmc_errors
10
rbcontrols_rows byrun order · 1 run

Highest 9 (run 1) · lowest 9 (run 1)

controls_rows by run
Runcontrols_rows
19
rderr_rows byrun order · 1 run

Highest 3 (run 2) · lowest 3 (run 2)

err_rows by run
Runerr_rows
23
replication holdoutfinal_candidates byrun order · 1 run

Highest 0 (run 1) · lowest 0 (run 1)

final_candidates by run
Runfinal_candidates
10
final mergefinal_candidates byrun order · 1 run

Highest 12 (run 1) · lowest 12 (run 1)

final_candidates by run
Runfinal_candidates
112
rd3rows byrun order · 1 run

Highest 12 (run 1) · lowest 12 (run 1)

rows by run
Runrows
112
safety2common_essential byrun order · 1 run

Highest 251 (run 1) · lowest 251 (run 1)

common_essential by run
Runcommon_essential
1251
pk5bn byrun order · 1 run

Highest 22 (run 1) · lowest 22 (run 1)

n by run
Runn
122
tcga2err_rows_final byrun order · 1 run

Highest 3 (run 1) · lowest 3 (run 1)

err_rows_final by run
Runerr_rows_final
13
stabilityboot_ci_excl0 byrun order · 1 run

Highest 20 (run 1) · lowest 20 (run 1)

boot_ci_excl0 by run
Runboot_ci_excl0
120
pk6n byrun order · 1 run

Highest 22 (run 1) · lowest 22 (run 1)

n by run
Runn
122
rnaipairs byrun order · 1 run

Highest 22 (run 1) · lowest 22 (run 1)

pairs by run
Runpairs
122
23 of 23 runs
RunParametersSeedStatusMetricsMachineDuration

Synthetic-lethality scan · reduce

Run1

fdr
0.1
mode
scan
shards
8
min_effect
-0.2
max_reports
120
failedShards
0
permutations
20
succeededShards
8
1Succeeded
tests
106,711
anchors
6
reports
24
controls
7
hits_kept
97
pairs_fdr
23
pairs_reused
0
anchors_reused
0
+6 more
1 vCPU · 4 GB2 min 12 s

show controls

Run2

—1000Succeeded
n_hits
97
n_final
24
n_controls
7
1 vCPU · 1 GB1 s

Synthetic-lethality scan · reduce

Run2

fdr
0.1
mode
scan
shards
8
min_effect
-0.2
max_reports
120
failedShards
0
permutations
20
succeededShards
8
1Succeeded
tests
12,165,001
anchors
684
reports
122
controls
7
hits_kept
7,681
pairs_fdr
2,369
pairs_reused
9
anchors_reused
6
+8 more
1 vCPU · 6 GB3 min 58 s

list candidates

Run1

—1000Succeeded
n_final
122
n_review
38
n_target
11
1 vCPU · 1 GB1 s

genecols

Run1

—1Succeeded
ncol
56
nrow
45,019
1 vCPU · 4 GB1 s

anchors_v2

Run2

del_thr
0.3
max_frac
0.3
min_lines
5
6Succeeded
cn_p1
0.4512
cn_p5
0.6062
del_thr
0.3
max_frac
0.3
cn_median
1.025
n_anchors
6,350
n_subtype
40
n_mutation
5,968
+11 more
1 vCPU · 4 GB16 min 42 s

confounder audit

Run2

nperm
200
7Succeeded
anchors
674
audited
7,681
hits_in
7,681
survive
1,902
flag_adj_weak
5,092
flag_neighbor
129
share_survive
0.2476
anchors_resolved
674
+3 more
1 vCPU · 4 GB17 min 60 s

expr_loss_v2

Run1

kit_inputs
["synleth_results_final.csv","synleth_hits.csv"]
11Succeeded
p_cut
0.0001
tests
55,357,302
models
1,292
n_perm
20
anchors
3,003
beta_cut
-0.2
max_frac
0.3
obs_hits
22,276
+15 more
4 vCPU · 12 GB23 min 4 s

drug replication v3

Run1

—1Succeeded
pairs_in
86
rows_gdsc
34
prism_rows
1,254,787
rows_prism
104
gdsc_mapped
241,578
tested_rows
113
novel_pairs_in
49
replicated_both
1
+2 more
1 vCPU · 4 GB3 min 34 s

sumd

Run1

—1000Succeeded
both
1
rows
113
gdsc_sig
11
prism_sig
3
novel_rows
35
novel_sig_any
4
both_rows_with_both_data
25
novel_genes_with_compound
5
1 vCPU · 4 GB1 s

novelty review

Run1

—1Succeeded
n_known
3
n_novel
37
pairs_in
49
pairs_out
49
string_nan
0
epmc_errors
0
n_uncertain
9
1 vCPU · 4 GB1 min 37 s

rb

Run1

—2Succeeded
new_unique
8,371
controls_rows
9
new_n_low_ge8
5,243
new_paralog_nokit
46
1 vCPU · 4 GB2 s

rd

Run1

—1000Succeeded
rows
49
novel_string_ge_0.4
0
1 vCPU · 4 GB1 s

replication holdout

Run3

—1Succeeded
ok
49
too_few
0
novel_in
37
pairs_in
49
pairs_out
49
unresolved
0
holdout_pass
26
final_candidates
0
+2 more
1 vCPU · 4 GB2 min 9 s

final merge

Run1

—1000Succeeded
rows
49
holdout_pass
26
final_candidates
12
novel_holdout_pass
20
with_drug_data_among_final
1
1 vCPU · 4 GB1 s

rd3

Run1

—1000Succeeded
rows
12
1 vCPU · 4 GB1 s

safety2

Run1

loeuf
0.35
gtex_tpm
200
1Succeeded
seconds
21.69
pairs_out
1,902
constrained
148
novel_pairs
22
sm_tractable
15
survivors_in
1,902
unique_genes
792
gtex_high_any
114
+10 more
1 vCPU · 4 GB26 s

pk5b

Run1

—1000Succeeded
n
22
1 vCPU · 1 GB1 s

tcga2

Run1

—2Succeeded
rows
416
studies
32
err_rows_final
3
1 vCPU · 4 GB33 s

stability

Run3

—11Succeeded
models
1,361
n_boot
1,000
tier_A
2
tier_B
10
tier_C
10
pairs_in
22
pairs_out
22
boot_ci_excl0
20
1 vCPU · 4 GB39 s

rd

Run2

—1Succeeded
pairs
12
err_rows
3
1 vCPU · 4 GB1 s

pk6

Run1

—1000Succeeded
n
22
1 vCPU · 4 GB1 s

rnai

Run2

—2Succeeded
pairs
22
tested
2
replicated
1
rnai_genes
17,309
rnai_lines
701
sign_agree
2
1 vCPU · 4 GB28 s

Start where others stopped.

Start freeExplore public research