20261002-2344 vs 20261002-0306

A (baseline) 20261002-2344 Haiku 4.5 (beta, ×1), agent agent_OHVSJI9Gd6gwsDnFSL-Xl · judge claude-code:claude-sonnet-4-6 · 146/146 completed · 0 failed · 0 missing · 0 ungraded · 0 no reference

B 20261002-0306 Haiku 4.5 (beta, ×1), agent agent_OHVSJI9Gd6gwsDnFSL-Xl · judge claude-code:claude-sonnet-4-6 · 146/146 completed · 0 failed · 0 missing · 0 ungraded · 0 no reference

146 questions asked in both runs, repeats pooled

Turns

	Expected	Completed	Failed	Missing	Ungraded	No reference	Eligible for recall
A	146	146	0	0	0	0	146
B	146	146	0	0	0	0	146

A turn is one question × repeat. Failed: an HTTP error or timeout. Missing: never recorded. Eligible turns are the graded, failed and missing turns of questions with a reference; failed and missing ones count as not passed. Ungraded turns are left out of recall until they're graded.

Headline

Metric	A	B	Δ (B − A)
Recall: passes / eligible turns (failed or missing = not passed)	64.4%	56.2%	-8.2 pp
Precision: passes / attempted answers	65.3%	56.9%	-8.3 pp
Attempt rate: attempted / eligible turns	98.6%	98.6%	0.0 pp
Pass rate over graded answers (report definition; failures left out)	64.4%	56.2%	-8.2 pp
Median latency, completed turns	24.3s	24.9s	+0.6s
p90 latency, completed turns	69.9s	67.0s	-2.8s
Median latency, completed + failed turns	24.3s	24.9s	+0.6s
p90 latency, completed + failed turns	69.9s	67.0s	-2.8s
Under 10s, of completed turns	8.9%	11.6%	+2.7 pp
Under 10s, of completed + failed turns	8.9%	11.6%	+2.7 pp
LLM calls / answer (mean)	8.11	8.35	+0.24
LLM calls / answer (median)	6.00	6.00	0.00
Tool rounds / answer (mean)	0.00	0.00	0.00
Successful handoffs / answer	0.00	0.00	0.00
Failed handoffs (total)	0	0	0
Tool error rate	4.7%	3.8%	-0.9 pp
Cost / answer	$0.061	$0.060	$-0.002

Recall = passes / eligible turns = precision × attempt rate. Precision = passes / attempted answers (pass or fail, not declined). Attempt rate = attempted / eligible turns. The report-style pass rate (passes / graded answers) leaves failed turns out and is shown for continuity with the per-run reports. p90 is the value at sorted index ⌊0.9·n⌋ (the maximum for n ≤ 10). Per question (recall across repeats): 15 better, 27 worse, 104 same. Green is better for B, red worse. Tool rounds and handoffs are only recorded in traces attached after the per-call trace change.

Consistency across repeats

	A	B
Questions with mixed pass/fail across repeats	0	0
Mean per-question pass variance (0 = always agrees, 0.25 = coin flip)	–	–
Median per-question latency stdev	–	–
Routed to (agent that wrote the answer)	–	–

By category

	Completed / expected A	B	Failed · missing · ungraded A	B	Recall A	B	Δ	Precision A	B	Attempt rate A	B	Median A	B	p90 A	B	Median incl. failed A	B	p90 incl. failed A	B	<10s A	B	LLM calls A	B
Study discovery	11 / 11	11 / 11	0 · 0 · 0	0 · 0 · 0	72.7%	81.8%	+9.1 pp	72.7%	81.8%	100.0%	100.0%	13.0s	14.0s	22.5s	21.1s	13.0s	14.0s	22.5s	21.1s	27.3%	36.4%	4.00	4.36
Cohort & clinical counts	13 / 13	13 / 13	0 · 0 · 0	0 · 0 · 0	92.3%	61.5%	-30.8 pp	92.3%	61.5%	100.0%	100.0%	18.8s	15.5s	72.4s	61.9s	18.8s	15.5s	72.4s	61.9s	15.4%	15.4%	8.15	6.69
Alteration frequency	36 / 36	36 / 36	0 · 0 · 0	0 · 0 · 0	61.1%	61.1%	0.0 pp	61.1%	62.9%	100.0%	97.2%	21.6s	18.4s	63.5s	56.3s	21.6s	18.4s	63.5s	56.3s	2.8%	13.9%	7.08	7.19
Variants & hotspots	16 / 16	16 / 16	0 · 0 · 0	0 · 0 · 0	62.5%	50.0%	-12.5 pp	62.5%	50.0%	100.0%	100.0%	26.6s	26.6s	53.4s	64.5s	26.6s	26.6s	53.4s	64.5s	0.0%	0.0%	8.31	7.94
Co-occurrence & exclusivity	8 / 8	8 / 8	0 · 0 · 0	0 · 0 · 0	37.5%	50.0%	+12.5 pp	37.5%	50.0%	100.0%	100.0%	37.2s	30.2s	69.9s	85.4s	37.2s	30.2s	69.9s	85.4s	0.0%	0.0%	8.88	10.12
Expression & multi-omics	20 / 20	20 / 20	0 · 0 · 0	0 · 0 · 0	60.0%	45.0%	-15.0 pp	63.2%	45.0%	95.0%	100.0%	38.4s	50.6s	135.5s	187.7s	38.4s	50.6s	135.5s	187.7s	5.0%	5.0%	12.65	13.60
Survival & outcomes	14 / 14	14 / 14	0 · 0 · 0	0 · 0 · 0	64.3%	64.3%	0.0 pp	69.2%	64.3%	92.9%	100.0%	57.0s	36.1s	87.8s	94.1s	57.0s	36.1s	87.8s	94.1s	7.1%	0.0%	11.29	11.07
Treatment	6 / 6	6 / 6	0 · 0 · 0	0 · 0 · 0	66.7%	50.0%	-16.7 pp	66.7%	50.0%	100.0%	100.0%	34.9s	54.4s	64.8s	141.0s	34.9s	54.4s	64.8s	141.0s	0.0%	0.0%	8.00	12.67
Patient & sample lookup	10 / 10	10 / 10	0 · 0 · 0	0 · 0 · 0	50.0%	50.0%	0.0 pp	50.0%	55.6%	100.0%	90.0%	19.6s	23.1s	71.9s	73.8s	19.6s	23.1s	71.9s	73.8s	10.0%	0.0%	7.20	6.90
Out of scope	12 / 12	12 / 12	0 · 0 · 0	0 · 0 · 0	75.0%	41.7%	-33.3 pp	75.0%	41.7%	100.0%	100.0%	11.8s	13.4s	41.0s	24.7s	11.8s	13.4s	41.0s	24.7s	33.3%	41.7%	3.67	3.75

By track

	Completed / expected A	B	Failed · missing · ungraded A	B	Recall A	B	Δ	Precision A	B	Attempt rate A	B	Median A	B	p90 A	B	Median incl. failed A	B	p90 incl. failed A	B	<10s A	B	LLM calls A	B
Data	62 / 62	62 / 62	0 · 0 · 0	0 · 0 · 0	67.7%	69.4%	+1.6 pp	67.7%	69.4%	100.0%	100.0%	19.6s	15.5s	48.1s	42.9s	19.6s	15.5s	48.1s	42.9s	9.7%	17.7%	6.10	6.32
Navigation	26 / 26	26 / 26	0 · 0 · 0	0 · 0 · 0	34.6%	30.8%	-3.8 pp	34.6%	33.3%	100.0%	92.3%	27.1s	26.0s	77.0s	64.5s	27.1s	26.0s	77.0s	64.5s	3.8%	0.0%	9.96	8.96
Analysis	46 / 46	46 / 46	0 · 0 · 0	0 · 0 · 0	73.9%	56.5%	-17.4 pp	77.3%	56.5%	95.7%	100.0%	47.0s	45.0s	87.8s	107.1s	47.0s	45.0s	87.8s	107.1s	4.3%	2.2%	10.93	11.93
Out of scope	12 / 12	12 / 12	0 · 0 · 0	0 · 0 · 0	75.0%	41.7%	-33.3 pp	75.0%	41.7%	100.0%	100.0%	11.8s	13.4s	41.0s	24.7s	11.8s	13.4s	41.0s	24.7s	33.3%	41.7%	3.67	3.75

Per question

Regressions first, then improvements, then unchanged. One mark per repeat: ✓ pass · ✗ fail · – declined · · no reference or ungraded · ! request failed · ? missing. “passes/eligible” after the marks. ⚠ marks a question asked or graded differently in A and B (compared only with --allow-mismatch).

Q	Category	A	B	Δ recall	Precision A	B	F · M · U A	B	Median A	B	p90 A	B	<10s A	B	Latency stdev B	LLM calls A	B	Routed to (B)	Question
4	Cohort & clinical counts	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	7.6s	5.3s	7.6s	5.3s	100.0%	100.0%	–	3.00	2.00	–	How many primary samples are in the MSK-CHORD Study?
9	Alteration frequency	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	42.9s	8.0s	42.9s	8.0s	0.0%	100.0%	–	12.00	2.00	–	"What are the top 5 frequently altered genes in the Osteosarcoma study from TARGET for mutations, copy numbers and SVs combined?"
14	Cohort & clinical counts	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	13.4s	13.7s	13.4s	13.7s	0.0%	0.0%	–	3.00	3.00	–	Which cancer type has the highest average tumor mutational burden across all studies?
16	Cohort & clinical counts	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	10.3s	22.2s	10.3s	22.2s	0.0%	0.0%	–	4.00	11.00	–	How many unique patients have both primary and metastatic samples in the MSK-CHORD Study?
18	Treatment	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	49.0s	67.0s	49.0s	67.0s	0.0%	0.0%	–	11.00	18.00	–	What are the most frequently administered systemic therapy regimens for lung cancer patients in the MSK-CHORD Study?
23	Cohort & clinical counts	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	72.4s	61.9s	72.4s	61.9s	0.0%	0.0%	–	15.00	11.00	–	What is the correlation between tumor mutational burden and microsatellite instability status in colorectal cancer patients from the MSK-CHORD Study?
28	Alteration frequency	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	22.0s	30.1s	22.0s	30.1s	0.0%	0.0%	–	7.00	9.00	–	"What percentage of glioblastoma patients have alterations in RB pathway genes (CDKN2A, CDK4, RB1)?"
43	Variants & hotspots	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	53.4s	64.6s	53.4s	64.6s	0.0%	0.0%	–	11.00	13.00	–	In the TCGA PanCancer Atlas endometrial cancer study, in samples with both KRAS and NRAS mutations, what is the distribution of variant allele frequencies suggesting clonal vs subclonal events?
47	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	31.9s	38.8s	31.9s	38.8s	0.0%	0.0%	–	5.00	8.00	–	How does ERBB2 mRNA expression vary across different cancer types in TCGA Pan-Cancer Atlas studies?
48	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	53.8s	58.1s	53.8s	58.1s	0.0%	0.0%	–	8.00	9.00	–	In the TCGA PanCancer Atlas breast cancer study, what is the concordance between ERBB2 copy number amplification, mRNA overexpression, and protein overexpression?
62	Cohort & clinical counts	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	58.7s	32.1s	58.7s	32.1s	0.0%	0.0%	–	16.00	10.00	–	In the TCGA Glioblastoma multiforme study compare the median patient age at diagnosis between patients with IDH1 R132H mutation and patients with wild-type IDH1.
64	Variants & hotspots	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	35.1s	26.4s	35.1s	26.4s	0.0%	0.0%	–	6.00	3.00	–	In TCGA PanCancer Atlas, which recurrent hotspot mutations occur almost exclusively in one cancer type?
66	Survival & outcomes	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	65.7s	58.5s	65.7s	58.5s	0.0%	0.0%	–	18.00	11.00	–	In colorectal cancer do patients with microsatellite instability in the TCGA dataset have a similar prognosis as those in the MSK Gastroenterology 2020 study?
76	Out of scope	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	9.0s	6.5s	9.0s	6.5s	100.0%	100.0%	–	1.00	1.00	–	Are TP53 mutations clinically actionable?
78	Out of scope	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	11.7s	14.6s	11.7s	14.6s	0.0%	0.0%	–	3.00	3.00	–	what's the best way to put clinical data into cbioportal?
79	Survival & outcomes	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	16.6s	19.4s	16.6s	19.4s	0.0%	0.0%	–	3.00	4.00	–	Can you please generate a survival curve for colorectal cancer patients based on the expression levels of IMPDH2?
81	Alteration frequency	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	25.6s	22.7s	25.6s	22.7s	0.0%	0.0%	–	6.00	5.00	–	tell me about IDH1 mutations in glioma
83	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	26.2s	33.3s	26.2s	33.3s	0.0%	0.0%	–	7.00	6.00	–	Help me rank TCGA cancer studies based on median CD3 expression
84	Out of scope	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	11.9s	12.3s	11.9s	12.3s	0.0%	0.0%	–	3.00	3.00	–	Can you analyze thyroid hormone gene expression by diagnosis in the Pediatric Brain Tumor Atlas (PBTA, Provisional) cohort?
91	Variants & hotspots	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	49.5s	64.5s	49.5s	64.5s	0.0%	0.0%	–	14.00	17.00	–	show me a histogram of C228T mutations in the tert promoter across cancer types
92	Variants & hotspots	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	22.7s	15.5s	22.7s	15.5s	0.0%	0.0%	–	6.00	4.00	–	what is the most prevalent TP53 mutation in uterine cancer that is not a point mutation
94	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	7.0s	7.9s	7.0s	7.9s	100.0%	100.0%	–	1.00	1.00	–	There is a heavily discussed driver alteration in MAP2K1 at codon 105 that significantly alters mRNA stability. Please list the expression values for the tumors that have a nucleotide change at this position
96	Survival & outcomes	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	9.2s	10.4s	9.2s	10.4s	100.0%	0.0%	–	2.00	2.00	–	Is KRAS G12C more aggressive than G12D?
108	Out of scope	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	13.2s	24.7s	13.2s	24.7s	0.0%	0.0%	–	2.00	11.00	–	Can you find a study that I may emulate that has a data_clinical_outcomes.txt file and associated meta file to interogate
113	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	135.5s	51.4s	135.5s	51.4s	0.0%	0.0%	–	25.00	9.00	–	In lower grade glioma, are there genes which are overexpressed in any of the molecular subtypes?
118	Expression & multi-omics	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	16.1s	10.4s	16.1s	10.4s	0.0%	0.0%	–	4.00	3.00	–	In TCGA lower grade glioma, show me IDH1 mRNA expression by IDH1 mutation status.
134	Alteration frequency	✓ 1/1	✗ 0/1	-100.0 pp	100.0%	0.0%	0 · 0 · 0	0 · 0 · 0	25.2s	10.1s	25.2s	10.1s	0.0%	0.0%	–	8.00	2.00	–	compare egfr mutations between lung and brain cancer
7	Alteration frequency	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	17.5s	11.7s	17.5s	11.7s	0.0%	0.0%	–	6.00	3.00	–	What are the top 5 most frequently copy number altered genes in the Osteosarcoma study from TARGET?
22	Survival & outcomes	– 0/1	✓ 1/1	+100.0 pp	–	100.0%	0 · 0 · 0	0 · 0 · 0	13.7s	37.1s	13.7s	37.1s	0.0%	0.0%	–	5.00	9.00	–	Do patients with PIK3CA mutations have different overall survival outcomes compared to PIK3CA wild-type patients in breast cancer from the MSK-CHORD Study?
29	Co-occurrence & exclusivity	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	30.9s	85.4s	30.9s	85.4s	0.0%	0.0%	–	8.00	24.00	–	"Are mutations in CDKN2A, CDK4, and RB1 mutually exclusive in glioblastoma patients?"
46	Variants & hotspots	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	24.8s	42.3s	24.8s	42.3s	0.0%	0.0%	–	7.00	13.00	–	Which cancer types show the highest frequency of BRAF V600E mutations across all TCGA Pan-Cancer Atlas studies?
55	Survival & outcomes	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	20.2s	21.8s	20.2s	21.8s	0.0%	0.0%	–	6.00	5.00	–	What is the median survival time in the Pediatric Neuroblastoma study from TARGET?
63	Expression & multi-omics	– 0/1	✓ 1/1	+100.0 pp	–	100.0%	0 · 0 · 0	0 · 0 · 0	12.0s	49.9s	12.0s	49.9s	0.0%	0.0%	–	2.00	10.00	–	In the TCGA PanCancer Atlas breast cancer study, what is the correlation coefficient between EGFR expression levels and PIK3CA mutation status considering only patients who also have a homozygous deletion of PTEN?
73	Alteration frequency	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	21.2s	19.8s	21.2s	19.8s	0.0%	0.0%	–	5.00	5.00	–	What is the frequency of TP53 mutations in lung cancer?
74	Alteration frequency	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	20.9s	14.7s	20.9s	14.7s	0.0%	0.0%	–	4.00	4.00	–	What are the most mutated genes in lung cancer?
102	Expression & multi-omics	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	21.5s	34.0s	21.5s	34.0s	0.0%	0.0%	–	5.00	13.00	–	calculate median expression of ceacam5, itgb6, muc2, tpgb and muc1 mRNA in pancreatic cancer
107	Study discovery	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	12.1s	14.0s	12.1s	14.0s	0.0%	0.0%	–	2.00	4.00	–	What kind of cancer are there in the database?
109	Variants & hotspots	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	11.9s	35.5s	11.9s	35.5s	0.0%	0.0%	–	2.00	9.00	–	I receive a report with the PIK3CA p.1069Wext3 mutation. Can you provide details of it
114	Expression & multi-omics	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	151.2s	113.0s	151.2s	113.0s	0.0%	0.0%	–	37.00	34.00	–	Are there differences in chromosome arm 7p copy number between lower grade glioma molecular subtypes?
117	Alteration frequency	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	14.2s	59.0s	14.2s	59.0s	0.0%	0.0%	–	4.00	25.00	–	What cancer types in MSK-IMPACT have mutations in TP53?
119	Survival & outcomes	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	34.4s	35.1s	34.4s	35.1s	0.0%	0.0%	–	8.00	5.00	–	In lower grade glioma, how do outcomes differ for IDH1 altered vs EGFR altered patients?
137	Cohort & clinical counts	✗ 0/1	✓ 1/1	+100.0 pp	0.0%	100.0%	0 · 0 · 0	0 · 0 · 0	37.0s	18.4s	37.0s	18.4s	0.0%	0.0%	–	11.00	5.00	–	In the TCGA Glioblastoma multiforme study (gbm_tcga_pan_can_atlas_2018), how many patients have an IDH1 R132H mutation and how many are IDH1 wild-type.
1	Study discovery	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	7.8s	7.8s	7.8s	7.8s	100.0%	100.0%	–	2.00	2.00	–	How many studies are in cBioPortal?
2	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	7.5s	7.3s	7.5s	7.3s	100.0%	100.0%	–	2.00	2.00	–	How many glioblastoma studies are in cBioPortal?
3	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	5.4s	5.8s	5.4s	5.8s	100.0%	100.0%	–	2.00	2.00	–	How many patients and samples are in the MSK-CHORD Study?
5	Treatment	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	13.1s	14.1s	13.1s	14.1s	0.0%	0.0%	–	3.00	3.00	–	What treatment did most patients receive in the MSK-CHORD Study?
6	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	16.5s	12.4s	16.5s	12.4s	0.0%	0.0%	–	5.00	4.00	–	What are the top 5 most frequently mutated genes in the Osteosarcoma study from TARGET?
8	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	12.5s	11.7s	12.5s	11.7s	0.0%	0.0%	–	5.00	4.00	–	What are the top 5 most frequently altered genes in a structural variant in the Osteosarcoma study from TARGET?
10	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	18.8s	11.7s	18.8s	11.7s	0.0%	0.0%	–	7.00	3.00	–	What is the median age at diagnosis for osteosarcoma patients in the TARGET study?
11	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	14.3s	8.7s	14.3s	8.7s	0.0%	100.0%	–	4.00	3.00	–	What are the top 5 most frequently mutated genes in the MSK-CHORD Study?
12	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	17.5s	15.5s	17.5s	15.5s	0.0%	0.0%	–	6.00	7.00	–	What is the most common cancer type in the MSK-CHORD Study based on sample count?
13	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	20.1s	56.3s	20.1s	56.3s	0.0%	0.0%	–	6.00	23.00	–	What percentage of patients in the MSK-CHORD Study have at least one TP53 mutation?
15	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	6.2s	5.0s	6.2s	5.0s	100.0%	100.0%	–	2.00	2.00	–	How many total studies contain mutation data in the cBioPortal database?
17	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	12.7s	14.7s	12.7s	14.7s	0.0%	0.0%	–	4.00	7.00	–	What are the top 5 most common primary diagnosis sites in the MSK-CHORD Study?
19	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	19.2s	17.0s	19.2s	17.0s	0.0%	0.0%	–	5.00	5.00	–	What are the top 10 most frequently mutated genes across all cancer types in the MSK-CHORD Study?
20	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	18.2s	57.6s	18.2s	57.6s	0.0%	0.0%	–	6.00	24.00	–	What percentage of colorectal cancer samples have KRAS mutations in the MSK-CHORD Study?
21	Co-occurrence & exclusivity	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	25.2s	24.5s	25.2s	24.5s	0.0%	0.0%	–	6.00	5.00	–	What are the most commonly co-occurring mutation pairs in breast cancer samples from the MSK-CHORD Study?
24	Treatment	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	15.5s	141.0s	15.5s	141.0s	0.0%	0.0%	–	4.00	24.00	–	Which genomic alterations are associated with immunotherapy response in melanoma patients from the MSK-CHORD Study?
25	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	50.8s	40.9s	50.8s	40.9s	0.0%	0.0%	–	6.00	5.00	–	How does the mutation landscape differ between primary and metastatic samples from the same patients in the MSK-CHORD Study?
26	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	19.3s	15.2s	19.3s	15.2s	0.0%	0.0%	–	6.00	5.00	–	What percentage of genomic events in the MSK-CHORD Study occur in genes that are off-panel (not covered by the sequencing panel used)?
27	Out of scope	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	62.3s	18.7s	62.3s	18.7s	0.0%	0.0%	–	15.00	5.00	–	Is there a correlation between ERBB2 gene amplification and ERBB2 protein expression levels in breast cancer samples from the MSK-CHORD Study?
30	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	51.9s	34.3s	51.9s	34.3s	0.0%	0.0%	–	11.00	7.00	–	In the TCGA PanCancer Atlas glioblastoma study, is CDK4 mRNA expression significantly higher in samples with CDK4 amplification compared to diploid samples?
31	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	20.5s	11.2s	20.5s	11.2s	0.0%	0.0%	–	5.00	2.00	–	Which cancer types have the highest frequency of EGFR mutations across all TCGA Pan-Cancer Atlas studies?
32	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	22.0s	25.0s	22.0s	25.0s	0.0%	0.0%	–	6.00	5.00	–	What are the most frequent EGFR mutation variants in lung adenocarcinoma and what percentage are known hotspot mutations?
33	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	15.7s	20.8s	15.7s	20.8s	0.0%	0.0%	–	5.00	5.00	–	What is the correlation coefficient between EGFR copy number and EGFR mRNA expression in ovarian cancer?
34	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	31.9s	17.5s	31.9s	17.5s	0.0%	0.0%	–	11.00	5.00	–	In the TCGA PanCancer Atlas ovarian cancer study, what is the correlation between EGFR mRNA expression and EGFR protein (RPPA) levels?
35	Expression & multi-omics	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	44.8s	52.0s	44.8s	52.0s	0.0%	0.0%	–	13.00	12.00	–	In the TCGA PanCancer Atlas ovarian cancer study, do samples with TP53 truncating mutations have significantly lower TP53 mRNA expression compared to wild-type samples?
36	Expression & multi-omics	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	60.3s	72.7s	60.3s	72.7s	0.0%	0.0%	–	16.00	17.00	–	Is BRCA1 promoter methylation associated with decreased BRCA1 mRNA expression in ovarian cancer?
37	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	67.4s	33.5s	67.4s	33.5s	0.0%	0.0%	–	11.00	7.00	–	Do ovarian cancer patients with BRCA1 or BRCA2 alterations have significantly different overall survival compared to wild-type patients?
38	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	168.5s	94.1s	168.5s	94.1s	0.0%	0.0%	–	29.00	21.00	–	Do lung adenocarcinoma patients with high EGFR mRNA expression (top quartile) have different survival outcomes than those with low expression?
39	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	68.4s	49.5s	68.4s	49.5s	0.0%	0.0%	–	8.00	9.00	–	"What are the survival differences between EGFR-mutated, EGFR-amplified, and EGFR wild-type lung adenocarcinoma patients?"
40	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	70.9s	43.6s	70.9s	43.6s	0.0%	0.0%	–	16.00	9.00	–	What are the most frequently altered genes in KRAS wild-type lung adenocarcinoma patients?
41	Expression & multi-omics	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	120.2s	191.9s	120.2s	191.9s	0.0%	0.0%	–	23.00	35.00	–	How does PTEN alteration (mutations or homozygous deletions) affect pAKT protein levels in lung squamous cell carcinoma?
42	Co-occurrence & exclusivity	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	38.9s	59.5s	38.9s	59.5s	0.0%	0.0%	–	9.00	13.00	–	In the TCGA PanCancer Atlas endometrial cancer study, what percentage of patients have co-occurring oncogenic mutations in both KRAS and NRAS?
44	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	83.8s	100.6s	83.8s	100.6s	0.0%	0.0%	–	19.00	17.00	–	What percentage of endometrial cancer samples have hypermutation (>5000 mutations) and how does this correlate with histological subtype?
45	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	63.5s	107.1s	63.5s	107.1s	0.0%	0.0%	–	12.00	21.00	–	What are the most frequently mutated genes in copy-number high subtype endometrial cancers compared to other subtypes?
49	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	31.9s	57.0s	31.9s	57.0s	0.0%	0.0%	–	8.00	12.00	–	Which cancer types have the highest aneuploidy scores and how does this correlate with mutation burden across TCGA Pan-Cancer studies?
50	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	29.3s	42.2s	29.3s	42.2s	0.0%	0.0%	–	6.00	7.00	–	"Are mutations in DNA repair pathway genes (BRCA1, BRCA2, ATM, CHEK2) enriched in specific cancer types across TCGA Pan-Cancer Atlas?"
51	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	26.4s	11.1s	26.4s	11.1s	0.0%	0.0%	–	6.00	3.00	–	What fraction of patients were older than five when diagnosed according to the Pediatric Neuroblastoma study from TARGET?
52	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	17.7s	15.6s	17.7s	15.6s	0.0%	0.0%	–	5.00	5.00	–	What is the most frequent mutation in the TP53 gene in the TCGA breast cancer study?
53	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	21.0s	6.3s	21.0s	6.3s	0.0%	100.0%	–	6.00	2.00	–	How many patients have an EGFR amplification in the TCGA Lung Adenocarcinoma study?
54	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	16.3s	15.3s	16.3s	15.3s	0.0%	0.0%	–	6.00	5.00	–	Which KRAS mutations are most common in colorectal cancer?
56	Treatment	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	35.8s	70.4s	35.8s	70.4s	0.0%	0.0%	–	9.00	15.00	–	In the TCGA glioblastoma study (Cell 2013), how does methylation of the MGMT gene promoter affect the prognosis and treatment response in patients with glioblastoma?
57	Out of scope	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	8.8s	7.9s	8.8s	7.9s	100.0%	100.0%	–	1.00	1.00	–	For patients with the EML4-ALK fusion gene in lung cancer how do the different fusion variants affect their long-term quality of life and risk of developing a secondary cancer?
58	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	68.7s	30.1s	68.7s	30.1s	0.0%	0.0%	–	14.00	7.00	–	In the “Pan-cancer analysis of whole genomes” study what is the survival difference and the corresponding statistical significance between patients with mutations in both TP53 and KRAS versus patients with only a KRAS mutation?
59	Out of scope	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	30.2s	51.3s	30.2s	51.3s	0.0%	0.0%	–	7.00	13.00	–	Are there studies that were not processed using polyA enrichment in order to explore lncRNA-related questions?
60	Expression & multi-omics	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	70.0s	52.1s	70.0s	52.1s	0.0%	0.0%	–	15.00	13.00	–	In the Breast Invasive Carcinoma TCGA study what are the top 5 down-regulated genes in TP53 mutated samples compared to non-mutated ones?
61	Survival & outcomes	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	44.8s	43.2s	44.8s	43.2s	0.0%	0.0%	–	12.00	11.00	–	In the Pediatric Neuroblastoma study from TARGET what is the survival difference and the corresponding statistical significance between patients who were older than four when diagnosed and the younger ones?
65	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	33.7s	42.1s	33.7s	42.1s	0.0%	0.0%	–	9.00	10.00	–	In the TCGA PanCancer Atlas breast cancer study, what is the average tumor mutational burden of patients who have at least two of the five most frequently mutated genes and how does this compare to the average TMB of all patients?
67	Co-occurrence & exclusivity	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	69.9s	52.7s	69.9s	52.7s	0.0%	0.0%	–	9.00	14.00	–	In the TCGA Breast Cancer study if a patient has both a PIK3CA mutation and a PTEN deletion what is their probability of having a luminal A subtype? Is this probability different from a patient with only a PIK3CA mutation?
68	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	40.4s	41.0s	40.4s	41.0s	0.0%	0.0%	–	6.00	7.00	–	What are the key genomic differences between lung adenocarcinomas and squamous cell carcinomas identified in the Pan-Lung Cancer TCGA study?
69	Patient & sample lookup	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	16.2s	14.9s	16.2s	14.9s	0.0%	0.0%	–	4.00	3.00	–	Which patients have a TP53 G199V mutation? Which are somatic vs germline?
70	Variants & hotspots	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	48.1s	29.2s	48.1s	29.2s	0.0%	0.0%	–	13.00	6.00	–	In MSS colorectal cancer, what is the frequency of BRAF oncogenic mutations (as defined by OncoKB)? Use the 2017 MSK study for this. Can you give me a table of all these mutations, with frequency, count and denominator?
71	Out of scope	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	20.6s	16.3s	20.6s	16.3s	0.0%	0.0%	–	3.00	2.00	–	What is the current and future support for storing and analyzing germline variants in cBioPortal, compared to other alternatives?
72	Study discovery	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	19.8s	28.9s	19.8s	28.9s	0.0%	0.0%	–	6.00	13.00	–	Is there any study with a polygenic risk score?
75	Patient & sample lookup	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	23.3s	25.3s	23.3s	25.3s	0.0%	0.0%	–	10.00	12.00	–	How many patients have a shallow deletion for SMARCA4 in the POG study?
77	Patient & sample lookup	✗ 0/1	– 0/1	0.0 pp	0.0%	–	0 · 0 · 0	0 · 0 · 0	23.1s	28.8s	23.1s	28.8s	0.0%	0.0%	–	8.00	9.00	–	can you show me the minerva viewer for the ohsu htan sample
80	Patient & sample lookup	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	71.9s	73.8s	71.9s	73.8s	0.0%	0.0%	–	14.00	11.00	–	Is there a cohort of NSCLC patient samples that have Kras mutations, wild-type p53, and high expression levels of c-Myc?
82	Treatment	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	64.8s	23.3s	64.8s	23.3s	0.0%	0.0%	–	11.00	7.00	–	How many GLASS patients developed hypermutation after TMZ treatment?
85	Alteration frequency	✗ 0/1	– 0/1	0.0 pp	0.0%	–	0 · 0 · 0	0 · 0 · 0	31.2s	31.4s	31.2s	31.4s	0.0%	0.0%	–	8.00	8.00	–	generate a oncoprint of kras, stk11, keap1, tp53 alterations stratified by smoking status in lung adenocarcinoma from the mskcc clincogenomic sequencing cohort. Please only select oncogenic somatic alterations and remove samples with unknown smoking status
86	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	42.8s	42.9s	42.8s	42.9s	0.0%	0.0%	–	13.00	15.00	–	what are the most common events in her2- breast cancer?
87	Patient & sample lookup	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	13.1s	14.5s	13.1s	14.5s	0.0%	0.0%	–	3.00	4.00	–	Show me cases where PALB2 or ATM have germline mutations
88	Out of scope	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	7.0s	6.4s	7.0s	6.4s	100.0%	100.0%	–	1.00	1.00	–	what do idh1 mutations do?
89	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	15.9s	21.1s	15.9s	21.1s	0.0%	0.0%	–	4.00	5.00	–	is there any imaging data?
90	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	57.2s	29.4s	57.2s	29.4s	0.0%	0.0%	–	15.00	7.00	–	show me the distribution of mutations in the tert promoter across cancer types
93	Patient & sample lookup	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	19.9s	12.5s	19.9s	12.5s	0.0%	0.0%	–	4.00	3.00	–	Find patients IDs and samples in colorectal cancer that harbor the V600V alteration in BRAF
95	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	21.9s	14.0s	21.9s	14.0s	0.0%	0.0%	–	7.00	3.00	–	download MSK-CHORD study on Non-Small Cell Lung Cancer dataset
97	Co-occurrence & exclusivity	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	38.4s	26.3s	38.4s	26.3s	0.0%	0.0%	–	9.00	7.00	–	give me a contingency table with the number of lung cancer patients with EGFR and/or KRAS alterations
98	Out of scope	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	7.6s	7.1s	7.6s	7.1s	100.0%	100.0%	–	1.00	1.00	–	Can you think of any flaws in the methodology used in the MSK-CHORD paper (Jee et al., Nature 2024)?
99	Out of scope	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	10.3s	6.9s	10.3s	6.9s	0.0%	100.0%	–	3.00	1.00	–	Can you help me write a production-ready Python script using Bokeh to build an interactive clinicogenomic dashboard to analyzing the MSK-CHORD dataset? I have some specific requirements I can give you
100	Patient & sample lookup	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	19.4s	20.9s	19.4s	20.9s	0.0%	0.0%	–	7.00	9.00	–	How many samples are there that have any of these mutations in SEPHS1: p.Arg371Trp, p.Arg371Gln, p.Arg371Gly?
101	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	11.4s	8.2s	11.4s	8.2s	0.0%	100.0%	–	3.00	2.00	–	List the top 20 mutated genes in study nbl_msk_2023.
103	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	70.7s	41.0s	70.7s	41.0s	0.0%	0.0%	–	4.00	4.00	–	in salivary cancer (adenoid cystic carcinoma), what are the expected drivers ? Classify them by actionability. What about BCOR mutations, either somatic or germline ?
104	Out of scope	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	41.0s	22.0s	41.0s	22.0s	0.0%	0.0%	–	4.00	3.00	–	write me python code that can query the timeline files for msk-chord
105	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	11.1s	9.4s	11.1s	9.4s	0.0%	100.0%	–	2.00	2.00	–	list the portal studies for pediatric cancers that were published in the last 5 years
106	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	23.8s	20.0s	23.8s	20.0s	0.0%	0.0%	–	6.00	6.00	–	Which studies have RNA expression for renal cancer?
110	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	54.9s	46.7s	54.9s	46.7s	0.0%	0.0%	–	12.00	8.00	–	Can you explore the difference in mutation frequency between left-sided and right-sided CRC?
111	Cohort & clinical counts	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	25.9s	18.0s	25.9s	18.0s	0.0%	0.0%	–	10.00	6.00	–	can you show me a study with longitudinal data and a patient that has multiple samples over time?
112	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	22.5s	14.8s	22.5s	14.8s	0.0%	0.0%	–	6.00	3.00	–	Which cBioPortal studies include lung adenocarcinoma samples with mutation and copy-number data?
115	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	83.8s	85.5s	83.8s	85.5s	0.0%	0.0%	–	23.00	23.00	–	Are there DNA methylation differences between lower grade glioma molecular subtypes?
116	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	16.4s	16.6s	16.4s	16.6s	0.0%	0.0%	–	5.00	5.00	–	What are the frequencies of different KRAS mutations in TCGA PanCan Lung Adenocarcinoma?
120	Co-occurrence & exclusivity	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	61.1s	32.4s	61.1s	32.4s	0.0%	0.0%	–	15.00	6.00	–	is there a relationship between cic mutation and 19q del in lgg?
121	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	23.6s	23.0s	23.6s	23.0s	0.0%	0.0%	–	8.00	7.00	–	In TCGA lower grade glioma, show me samples with EGFR gains.
122	Patient & sample lookup	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	9.7s	11.3s	9.7s	11.3s	100.0%	0.0%	–	3.00	3.00	–	In TCGA lower grade glioma, filter to samples that are both IDH1 and TP53 mutant and show me the summary page.
123	Patient & sample lookup	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	14.3s	33.1s	14.3s	33.1s	0.0%	0.0%	–	3.00	7.00	–	In TCGA lower grade glioma, show me samples that are TP53 mutant or EGFR amplified.
124	Expression & multi-omics	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	28.3s	18.3s	28.3s	18.3s	0.0%	0.0%	–	5.00	3.00	–	show me EGFR expression across cancer types
125	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	28.5s	13.3s	28.5s	13.3s	0.0%	0.0%	–	9.00	3.00	–	show me point mutations in EGFR in lung cancer
126	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	19.3s	13.4s	19.3s	13.4s	0.0%	0.0%	–	6.00	5.00	–	are there cdkn2a het losses in gbm tcga study?
127	Patient & sample lookup	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	45.5s	26.2s	45.5s	26.2s	0.0%	0.0%	–	16.00	8.00	–	show me gbm with mgmt hypermethylation
128	Study discovery	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	13.0s	15.3s	13.0s	15.3s	0.0%	0.0%	–	5.00	6.00	–	Is there a lower grade glioma study with race data?
129	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	87.8s	67.7s	87.8s	67.7s	0.0%	0.0%	–	14.00	11.00	–	compare atrx mutant vs cic mutant lgg - are there different outcomes?
130	Survival & outcomes	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	64.8s	33.3s	64.8s	33.3s	0.0%	0.0%	–	15.00	9.00	–	are there different outcomes for idh1 mutant vs egfr amp in lgg?
131	Co-occurrence & exclusivity	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	27.3s	28.0s	27.3s	28.0s	0.0%	0.0%	–	6.00	5.00	–	what other genes are altered in kras mutant crc or luad
132	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	25.3s	15.0s	25.3s	15.0s	0.0%	0.0%	–	3.00	4.00	–	Create an OncoPrint with a merged track for the EGFR family genes (EGFR, ERBB2, ERBB3, ERBB4) across TCGA PanCancer Atlas studies.
133	Alteration frequency	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	17.2s	15.2s	17.2s	15.2s	0.0%	0.0%	–	5.00	4.00	–	What are the EGFR mutation frequencies across cancer types in the MSK-IMPACT 50K study?
135	Survival & outcomes	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	49.2s	125.4s	49.2s	125.4s	0.0%	0.0%	–	13.00	44.00	–	How does overall survival compare between prostate cancer patients where TMPRSS2 is acting as the upstream donor to an ERG fusion event and patients without this fusion?
136	Co-occurrence & exclusivity	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	36.0s	27.8s	36.0s	27.8s	0.0%	0.0%	–	9.00	7.00	–	In the TCGA Breast Cancer study, do TP53 mutations and high MYC expression co-occur or are they mutually exclusive?
138	Variants & hotspots	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	29.8s	25.8s	29.8s	25.8s	0.0%	0.0%	–	9.00	7.00	–	show me all KRAS mutations in colorectal cancer that are not at position 12
139	Variants & hotspots	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	51.8s	26.7s	51.8s	26.7s	0.0%	0.0%	–	17.00	9.00	–	show me cholangio with idh1 mutations other than r132
140	Variants & hotspots	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	62.8s	43.0s	62.8s	43.0s	0.0%	0.0%	–	12.00	10.00	–	what's the frequency of different idh1 mutations in glioma vs cholangio vs chndrosarcoma? Give me a link to compare the frequency of the specific IDH1 mutations in those cancer types.
141	Expression & multi-omics	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	111.2s	187.7s	111.2s	187.7s	0.0%	0.0%	–	29.00	47.00	–	is there a relatinoship between mgmt methylation and idh1 mutation in glioma?
142	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	12.3s	12.6s	12.3s	12.6s	0.0%	0.0%	–	3.00	3.00	–	Give me an OncoPrint for RTK genes in lung cancer, limited to driver events.
143	Variants & hotspots	✓ 1/1	✓ 1/1	0.0 pp	100.0%	100.0%	0 · 0 · 0	0 · 0 · 0	17.7s	32.0s	17.7s	32.0s	0.0%	0.0%	–	5.00	13.00	–	show me P135L mutations in $p14^{ARF}$
144	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	77.0s	16.3s	77.0s	16.3s	0.0%	0.0%	–	18.00	4.00	–	are lung carcinosarcomas associated with BRIP1 mutations?
145	Alteration frequency	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	7.8s	8.4s	7.8s	8.4s	100.0%	100.0%	–	2.00	2.00	–	Which genes are enriched for mutations between NSCLC vs squamous cell carcinoma?
146	Treatment	✗ 0/1	✗ 0/1	0.0 pp	0.0%	0.0%	0 · 0 · 0	0 · 0 · 0	34.1s	41.7s	34.1s	41.7s	0.0%	0.0%	–	10.00	9.00	–	In the MSK-CHORD study, is it possible to see which patients received radiation therapy?