Results

Conroy JM1,2, Pabla S1, Johanns T3, Glenn ST1,2, Nesline M1, Burgher B1, Lenzo, FL1, Kato S4, Kurzrock R4, Papanicolau-Sengos A1, Gardner M1, Morrison CD1,2*OmniSeq, Inc1, Buffalo, NY; Roswell Park Comprehensive Cancer Center2, Buffalo, NY; Washington University School of Medicine3, St. Louis, MO; UCSD School of Medicine4, San Diego, CA

ASCO-SITC 2019 – P27

Tumor Mutational Burden (TMB): Assessment of Inter- and Intra-tumor heterogeneity

700 Ellicott Street | Buffalo NY, 14203

Methods

Background

Results and Conclusions

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Following anatomical pathologist review, DNA was isolatedfrom resection or needle core biopsy FFPE specimenscollected from 36 cancer patients. Two to six specimens perpatient, including primary, recurrent and metastatic caseswith neoplastic content, percent necrosis and tissueamounts representative of typical clinical samples wereprocured. TMB was evaluated by performing targeted NGSusing a 409 gene panel from 30ng of DNA (Figure 1). TMBwas determined and reported as non-synonymousmutations per megabase DNA (Muts/Mb).

As an emerging biomarker, tumor mutational burden (TMB)is associated with response to immune checkpointinhibitors. The tumor tissue selected for molecular analysiscould be critical for accurate TMB assessment andtherapeutic selection. We evaluated TMB and the tumorspecimen tested to determine the extent tissue selectionand specimen characteristics affect TMB analysis.

Specimens

• Inter- and intra-tumor TMB variation occurs, but in <15% ofpatients tested

• Spatial and temporal differences in specific mutations that makeup TMB is common

• Sample selection and pre-analytical pathologist review is criticalfor TMB evaluation

• Clinical interpretation of TMB will need to factor in multi-sitesequencing, influence of treatment and neo-antigenicity

Figure 1: TMB NGS Workflow

Nine patients had multiple specimens from the samesurgical event (Figure 2) for which a subset of tumors wereevaluated for intra-tumor (spatial) heterogeneity. Anadditional 27 patients had specimens from multiple surgicalevents and anatomical sites spanning up to seven years(Figure 3). In total, 98 specimens were evaluated for TMBfor 36 inter-patient comparisons (Figure 4) representinginter-tumor, intra-tumor and intra/inter-tumor comparisons(Figure 5). The percentage of common variant overlap withintumors was calculated for each subject.

For each patient, the heterogeneity of TMB values withintumors (spatial), between tumors (spatial and temporal),and across collection times was assessed (Figures 6 and 7).Over representation analysis (v-test) was performed todetermine association of TMB variation with specimencharacteristics including collection time, necrosis, tumoramount (mm2), neoplastic content and PMR (Figure 8).

Figure 2: Tumors from 9 patientscollected at a single surgical event withTMB evaluated within a tumor (Site 1)and between tumors (sites 1-4).

Table 1: Tumor samples from 36 patientsevaluated for TMB. Patient’s with red arrows() are represented in figure 5. Specimencharacteristics were determined by microscopicanatomical pathologist review.

Patient 17

Patient 19Patient 20Patient 21Patient 22Patient 23Patient 24Patient 36

Patient 18

Site 1 Site 2 Site 3 Site 4

Patients with both intra- and inter-tumor samples from single surgical event (spatial)

OvarianColon UterinePancreatic

Primary Metastatic

Patients with inter-tumor samples from multiple surgical events (temporal)

Figure 3: Tumors from 27 patientscollected from multiple surgicalevents and anatomical sites with TMBevaluated across several timepoints.

TMB Comparison Patient numberInter1 vs Inter2 24Inter1 vs Inter2 vs Inter3 4Intra1 vs Intra1 4Inter1 vs Intra1 1Inter1 vs Inter2 vs Intra1 1Inter2 vs Inter3 vs Intra1 2

Figure 4: Comparisons for 36patients evaluating intra-tumor andinter-tumor TMB heterogeneity.

Pt ID ComparisonTMB

ValueNeoplastic nuclei (%)

Necrosis (%)

Tissue amount (mm2)

Order of resection or biopsy Cancer type PMR Site

Time between collections (months)

Variant Overlap

Inter2 8.9 90 0 150 2 Melanoma Metastatic Skin 9Inter1 8.0 80 0 50 1 Melanoma Metastatic Lymph node 0Inter2 2.6 70 35 125 2 Bladder Recurrence Bladder 21Inter1 3.5 40 0 70 1 Bladder Primary Bladder 0Inter3 7.1 50 0 3 3 Bladder Metastatic Soft Tissue 32Inter1 3.6 95 15 200 1 Melanoma Metastatic Brain 0Inter2 4.6 70 0 130 2 Melanoma Metastatic Small bowel 19Inter2 8.7 60 5 110 2 Melanoma Metastatic Peritoneum 14Inter1 11.4 90 0 110 1 Melanoma Metastatic Mesentery 0Inter2 7.0 70 0 125 2 Bladder Metastatic Lung 35Inter1 7.9 90 0 80 1 Bladder Primary Bladder 0Inter2 4.4 90 0 90 2 Melanoma Metastatic Soft Tissue 6Inter3 6.1 90 0 125 3 Melanoma Metastatic Soft Tissue 9Inter1 5.3 95 0 100 1 Melanoma Metastatic Skin 0Inter2 7.0 55 0 100 2 Lung Metastatic Lung 86Inter1 7.0 45 5 70 1 Lung Primary Lung 0Inter2 6.2 95 0 150 2 Melanoma Metastatic Small bowel 25Inter1 6.1 90 0 75 1 Melanoma Metastatic Lymph node 0Inter1 5.3 90 0 150 2 Melanoma Metastatic Skin 0Inter2 4.4 85 0 110 1 Melanoma Metastatic Lymph node 6Inter3 5.3 60 0 100 3 Melanoma Metastatic Skin 16Inter1 51.6 50 0 100 1 Melanoma Primary Skin 0Inter2 28.5 45 0 25 2 Melanoma Metastatic Lung 34Inter2 7.0 80 0 130 2 Lung Metastatic Brain 48Inter1 7.0 50 0 60 1 Lung Primary Lung 0Inter2 0.9 20 0 5 2 Melanoma Metastatic Liver 5Inter1 12.3 90 0 50 1 Melanoma Metastatic Lymph node 0Inter2 5.3 90 0 90 2 Kidney Metastatic Adrenal gland 8Inter1 4.4 85 0 200 1 Kidney Metastatic Lung 0Inter2 2.7 70 15 125 2 Lung Metastatic Brain 9Inter1 0.0 25 0 125 1 Lung Primary Lung 0Inter1 6.2 90 0 100 1 Melanoma Metastatic Head & Neck 0Inter2 6.2 90 0 250 2 Melanoma Metastatic Skin 9Inter2 5.3 90 0 120 2 Melanoma Metastatic Brain 9Inter1 3.5 40 0 100 1 Melanoma Metastatic Lymph node 0Intra1 9.7 90 0 200 1 Colon Metastatic Liver 0Intra1 9.7 80 0 200 1 Colon Metastatic Liver 0Intra1 10.6 80 10 150 1 Colon Metastatic Liver 0Intra1 10.7 85 5 300 1 Colon Metastatic Liver 0Intra1 5.3 90 35 200 1 Ovarian Metastatic Adrenal gland 0Intra1 5.3 85 35 300 1 Ovarian Metastatic Adrenal gland 0Intra1 5.3 80 35 150 1 Ovarian Metastatic Adrenal gland 0Intra1 6.2 70 35 300 1 Ovarian Metastatic Adrenal gland 0Intra1 3.5 90 35 300 1 Ovarian Metastatic Adrenal gland 0Intra1 2.0 70 5 250 1 Colon Metastatic Liver 0Intra1 2.7 80 10 300 1 Colon Metastatic Liver 0Inter1 3.6 45 15 100 2 Colon Metastatic Liver 0Intra1 2.7 70 5 200 1 Colon Metastatic Liver 0Intra1 0.9 80 0 90 1 Ovarian Primary Ovary 0Intra2 1.8 45 0 200 1 Ovarian Metastatic Omentum 0Inter1 1.8 40 0 110 2 Ovarian Metastatic Stomach 0Intra1 0.0 85 0 175 3 Ovarian Primary Ovary 0Intra2 2.6 70 0 175 1 Ovarian Metastatic Omentum 0Intra1 4.4 95 0 250 1 Ovarian Primary Ovary 0Inter3 4.4 70 0 10 1 Ovarian Metastatic Peritoneum 0Intra1 3.5 85 5 250 1 Ovarian Primary Ovary 0Intra1 3.5 90 0 250 1 Ovarian Primary Ovary 0Inter2 3.5 85 0 200 1 Ovarian Metastatic Peritoneum 0Inter1 2.7 60 5 300 1 Colon Metastatic Colorectal 0Intra1 2.7 75 5 125 1 Colon Metastatic Ovary 0Inter3 3.5 30 5 300 1 Colon Metastatic Soft Tissue 0Intra1 3.5 30 25 250 1 Colon Metastatic Ovary 0Intra1 4.4 85 10 175 1 Colon Metastatic Ovary 0Inter2 2.7 30 5 175 1 Colon Metastatic Peritoneum 0Intra1 2.7 90 0 300 1 Uterine Primary Uterine 0Intra1 3.5 90 0 110 1 Uterine Primary Uterine 0Intra1 4.4 70 15 350 1 Uterine Primary Uterine 0Intra1 2.7 90 5 350 1 Uterine Primary Uterine 0Intra1 4.4 90 5 200 1 Pancreatic Primary Pancreas 0Intra1 6.2 90 0 150 1 Pancreatic Primary Pancreas 0Intra1 8.8 70 0 200 1 Pancreatic Primary Pancreas 0Intra1 10.7 90 0 300 1 Pancreatic Primary Pancreas 0Intra1 8.0 90 0 300 1 Pancreatic Primary Pancreas 0Inter1 22.9 85 0 300 1 Melanoma Metastatic Parotid gland 0Inter2 25.5 80 0 250 2 Melanoma Metastatic Lymph node 29Inter1 14.9 20 0 5 1 Melanoma Metastatic Bone 0Inter2 62.8 70 40 125 2 Melanoma Metastatic Bone 13Inter1 1.8 80 0 125 1 Melanoma Metastatic Soft tissue 0Inter2 1.8 80 0 300 2 Melanoma Metastatic Lymph node 5Inter1 9.7 25 5 300 1 Melanoma Metastatic Breast 0Inter2 9.7 85 0 25 2 Melanoma Metastatic Lung 29Inter1 1.8 40 0 400 1 Melanoma Metastatic Skin 0Inter2 4.4 25 0 250 2 Melanoma Metastatic Skin 49Inter1 7.9 60 0 80 1 Melanoma Metastatic Skin 0Inter2 4.4 20 0 40 2 Melanoma Metastatic Soft tissue 13Inter1 5.3 80 0 100 1 Melanoma Metastatic Lymph node 0Inter2 4.4 90 0 110 2 Melanoma Metastatic Soft tissue 6Inter1 1.7 55 0 125 1 Melanoma Metastatic Lymph node 0Inter2 1.8 80 0 20 2 Melanoma Metastatic Skin 13Inter1 6.1 80 0 50 1 Melanoma Metastatic Skin 0Inter2 2.6 90 0 35 2 Melanoma Metastatic Skin 5Inter1 3.5 90 0 20 1 Melanoma Metastatic Spleen 0Inter2 4.4 80 0 300 2 Melanoma Metastatic Soft tissue 8Inter1 29.8 80 10 10 1 Colon Metastatic Liver 0Inter2 39.3 90 0 10 2 Colon Metastatic Liver 8Inter1 3.6 90 50 5 1 Colon Primary rectum 0Inter2 38.7 50 10 7 1 Colon Primary colon 0Inter3 24.3 50 0 10 1 Colon Primary colon 0

Patient 36

Patient 35

Patient 34

Patient 33

Patient 32

Patient 26

Patient 25

Patient 24

Patient 23

Patient 22

Patient 31

Patient 30

Patient 29

Patient 28

Patient 27

Patient 16

Patient 21

Patient 20

Patient 19

Patient 18

Patient 17

Patient 11

Patient 12

Patient 13

Patient 14

Patient 15

Patient 6

Patient 7

Patient 8

Patient 9

Patient 10

Patient 1

Patient 2

Patient 3

Patient 4

Patient 5

67%

75%

0%

7%

57%

45%

73%

75%

29%

64%

89%

56%

14%

40%

71%

0%

83%

73%

67%

67%

40%

63%

33%

33%

36%

74%

15%

100%

76%

3%

40%

27%

57%

100%

43%

29%

Figure 6: TMB variationbetween inter-tumor andintra-tumor specimensacross all specimens.

Figure 7: TMB variationbetween tumors within apatient (circles) across time.

Inter-tumor TMB

Intra-tumor TMB

Figure 5: Representative multi-specimen TMB comparisons. Top =Inter-tumor. Bottom left = Intra-tumor. Bottom right = Intra-and inter-tumor. Variant overlap is % of commonly detected mutations used todetermine TMB value.

Intra-and inter-tumor TMB

Inter-tumor TMB

Figure 8: TMB variationwithin a patient is mostinfluenced by tissue amount.

Patient 25

Patient 10

Patient 36

Patient 7

Patient 17

Patient 24

Patient 21

Patient 22