Aditya Rajan,1 Sahil Tonk,1 Chhanda Bose,1 Sharda P. Singh,1* Sriman Swarup,1 Santosh Chavali, Kishore Bhende,2 Philip T. Palade,3 Ashly Hindle,1 Meenakshi Darden,4 Vijay Tonk,2* and Sanjay Awasthi1*
1Division of Hematology & Oncology, 1Department of Internal Medicine, 1School of Medicine, 2Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, 3Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, 4McGovern Medical School of the University of Texas Health Sciences Center, Houston TX, 77030
Listing of Supplemental Material(s):
Supplemental Table 1. Raw data and pivot table (Provided as an EXCEL File).
Supplemental Table 2. Most common loci altered in ALL patients by sex.
Supplemental Table 3. Most common loci altered in sarcoma patients by sex.
Supplemental Table 4. Most common loci altered in lymphoma patients by sex.
Supplemental Table 5. Most common loci altered in Wilm’s tumor patients by sex.
Supplemental Table 6. Most common loci altered in neuroblastoma patients by sex.
Supplemental Table 7. Amplifications and Deletions at 8p11.22, (ADAM32, TACC1 and TM2D2): Gains (amplifications) and Losses (deletions) and no. of cases with rearrangement are listed by diagnosis.
Supplemental Table 8. Amplifications and Deletions at 15q11.1-15q11.2: Gains (amplifications) and Losses (deletions) and no. of cases with rearrangement are listed by diagnosis.
Supplemental Table 9. Amplifications and Deletions at 8p23.1: Gains (amplifications) and Losses (deletions) and no. of cases that had the rearrangement are listed by diagnosis.
Supplemental Table 10. Amplifications and Deletions at 14q11.2, 22481496-22974566: Gains (amplifications) and Losses (deletions) and no. of cases that had the rearrangement are listed by diagnosis.
Supplemental Table 11. Amplifications and Deletions at 14q11.2, 20203456-20331146: Gains (amplifications) and Losses (deletions) and no. of cases that had the rearrangement are listed by diagnosis.
Supplemental Table 2. Most common loci altered in ALL patients by sex
| Chromosomal Loci | No. Female ALL | No. Male ALL | Total No. ALL Alterations |
| 14q32.33 | 17 | 21 | 38 |
| 14q11.2 | 10 | 19 | 29 |
| 8p11.22 | 11 | 9 | 20 |
| 8p23.1 | 9 | 10 | 19 |
| 2p11.2 | 5 | 7 | 12 |
| 15q11.1q11.2 | 7 | 5 | 12 |
| Xp22.33q28 | 3 | 5 | 8 |
| 22q11.22 | 4 | 4 | 8 |
| 15q11.2 | 6 | 2 | 8 |
Supplemental Table 3. Most common loci altered in sarcoma patients by sex
| Chromosomal Loci | No. Female Sarcoma | No. Male Sarcoma | Total No. of Sarcoma Alterations |
| 8p23.1 | 4 | 14 | 18 |
| 14q32.33 | 7 | 11 | 18 |
| 14q11.2 | 4 | 10 | 14 |
| 8p11.22 | 7 | 9 | 16 |
| 17q12 | 1 | 6 | 7 |
| 1q21.1 | 0 | 5 | 5 |
| 10q11.22 | 0 | 4 | 4 |
| 10q26.13 | 3 | 4 | 7 |
| 21p11.2p11.1 | 0 | 4 | 4 |
| 5q13.2 | 1 | 4 | 5 |
| 17q11.2 | 2 | 3 | 5 |
| 22q11.1 | 2 | 3 | 5 |
| 22q12.1 | 1 | 3 | 4 |
| 7q11.23 | 0 | 3 | 3 |
Supplemental Table 4. Most common loci altered in lymphoma patients by sex
| Chromosomal Loci | No. Female Lymphoma | No. Male Lymphoma | Total No. Lymphoma alterations |
| 14q32.33 | 2 | 6 | 8 |
| 8p11.22 | 2 | 5 | 7 |
| 14q11.2 | 2 | 4 | 6 |
| 8p23.1 | 1 | 5 | 6 |
| 1q23.3 | 0 | 3 | 3 |
| 7q34 | 1 | 2 | 3 |
Supplemental Table 5. Most common loci altered in Wilm’s tumor patients by sex
| Chromosomal Loci | No. Female Wilm’s tumor | No. Male Wilm’s tumor | Total No. Wilm’s tumor alterations |
| 14q32.33 | 3 | 2 | 5 |
| 8p11.22 | 2 | 2 | 4 |
| 8p23.2 | 0 | 4 | 4 |
| 16q11.2q24.3 | 2 | 1 | 3 |
| 1q21.1q44 | 0 | 3 | 3 |
| 2q13 | 3 | 0 | 3 |
| 4p16.3q35.2 | 2 | 1 | 3 |
Supplemental Table 6. Most common loci altered in neuroblastoma patients by sex
| Chromosomal Loci | No. Female Neuroblastoma | No. Male Neuroblastoma | Total No. Neuroblastoma alterations |
| 14q32.33 | 4 | 2 | 6 |
| 8p23.1 | 1 | 5 | 6 |
| 10q26.13 | 1 | 4 | 5 |
| 14q11.2 | 1 | 4 | 5 |
| 8p11.22 | 3 | 2 | 5 |
| 15q11.1q11.2 | 0 | 4 | 4 |
| 17q11.2 | 0 | 4 | 4 |
| 2p24.3 | 1 | 3 | 4 |
Supplemental Table 7. Amplifications and Deletions at 8p11.22, (ADAM32, TACC1 and TM2D2): Gains (amplifications) and Losses (deletions) and no. of cases with rearrangement are listed by diagnosis
| DX | No. Cases | No. Gain | No. Loss |
| ALL | 20 | 18 | 2 |
| Neuroblastoma | 5 | 5 | 0 |
| Bone Tumor | 4 | 2 | 2 |
| Wilm’s Tumor | 4 | 4 | 0 |
| Breast Tumor | 5 | 5 | 0 |
| Myeloid Neoplasm | 3 | 2 | 1 |
| Fibromatosis | 2 | 2 | 0 |
| Abnormal Monocytosis | 1 | 1 | 0 |
| Lymphoma | 7 | 6 | 1 |
| Rhabdomyosarcoma | 2 | 2 | 0 |
| Pancytopenia | 3 | 2 | 1 |
| Other Leukemia | 2 | 2 | 0 |
| Testicular Cancer | 1 | 1 | 0 |
| Hepatocellular Cancer | 1 | 1 | 0 |
| Medulloblastoma | 1 | 1 | 0 |
| Giant Cell Bone Tumor | 1 | 0 | 1 |
| Osteosarcoma | 1 | 1 | 0 |
| Chondroblastoma | 1 | 0 | 1 |
| Oral Lesion | 1 | 0 | 1 |
| Rectal Polyp | 1 | 0 | 1 |
| Chest mass | 1 | 1 | 0 |
| Neutropenia | 1 | 0 | 1 |
| Other Tumors | 4 | 3 | 1 |
| Other conditions | 11 | 8 | 3 |
Supplemental Table 8. Amplifications and Deletions at 15q11.1-15q11.2: Gains (amplifications) and Losses (deletions) and no. of cases with rearrangement are listed by diagnosis
| DX | No. Cases | No. Gain | No. Loss |
| ALL | 26 | 9 | 17 |
| Neuroblastoma | 7 | 5 | 2 |
| Brain Tumor | 3 | 3 | 0 |
| Breast Mass | 3 | 0 | 3 |
| Myeloid Neoplasm | 2 | 1 | 1 |
| Other Leukemia | 2 | 1 | 1 |
| Lymphoma | 3 | 1 | 2 |
| Bone Tumor | 4 | 1 | 3 |
| Osteosarcoma | 2 | 1 | 1 |
| Cytopenia | 5 | 3 | 2 |
| Oral Lesion | 2 | 0 | 2 |
| Ewing Sarcoma | 1 | 0 | 1 |
| Medulloblastoma | 1 | 1 | 0 |
| Peripheral Neural Epithelioma | 1 | 0 | 1 |
| Renal Cell Carcinoma | 1 | 0 | 1 |
| Rectal Polyp | 1 | 0 | 1 |
| Neutropenia | 1 | 1 | 0 |
| Hepatocellular Carcinoma | 1 | 0 | 1 |
| Melanoma | 1 | 0 | 1 |
| Other Tumors/Masses | 6 | 1 | 5 |
| Other Conditions | 10 | 2 | 8 |
Supplemental Table 9. Amplifications and Deletions at 8p23.1: Gains (amplifications) and Losses (deletions) and no. of cases which had the rearrangement are listed by diagnosis
| DX | No. Cases | No. Gain | No. Loss |
| ALL | 13 | 2 | 11 |
| Other Acute Leukemia | 4 | 1 | 3 |
| Neuroblastoma | 6 | 1 | 5 |
| Fibromatosis | 4 | 0 | 4 |
| Bone tumor | 6 | 3 | 3 |
| Lymphoma | 4 | 0 | 4 |
| Breast Mass | 2 | 0 | 2 |
| Osteosarcoma | 2 | 0 | 2 |
| Other Sarcoma | 3 | 2 | 1 |
| Thyroid Nodule | 2 | 0 | 2 |
| Hepatocellular Cancer | 2 | 0 | 2 |
| Ovarian | 2 | 0 | 2 |
| Renal | 2 | 0 | 2 |
| Cytopenia | 4 | 1 | 3 |
| Testicular Tumor | 1 | 1 | 0 |
| Abnormal Testes | 2 | 0 | 2 |
| Chest Mass | 1 | 0 | 1 |
| Chondroid tumor | 2 | 1 | 1 |
| Chondroblastoma | 1 | 0 | 1 |
| Rectal Mass | 1 | 0 | 1 |
| Langerhan’s Disease | 1 | 1 | 0 |
| Arm Mass | 1 | 1 | 0 |
| Other Benign Tumor | 3 | 0 | 3 |
| Other conditions | 9 | 3 | 6 |
Supplemental Table 10. Amplifications and Deletions at 14q11.2, 22481496-22974566: Gains (amplifications) and Losses (deletions) and no. of cases that had the rearrangement are listed by diagnosis
| DX | No. Cases | No. Gain | No. Loss |
| ALL | 15 | 11 | 4 |
| Neuroblastoma | 4 | 4 | 0 |
| Lymphoma | 4 | 3 | 1 |
| Bone Tumor | 2 | 2 | 0 |
| Fibromatosis | 2 | 1 | 1 |
| Wilm’s Tumor | 2 | 2 | 0 |
| Oral Lesion | 2 | 2 | 0 |
| Other Leukemia | 1 | 1 | 0 |
| Medulloblastoma | 1 | 1 | 0 |
| Renal Cell Carcinoma | 1 | 1 | 0 |
| Melanoma | 1 | 1 | 0 |
| Testicular Tumor | 1 | 1 | 0 |
| Ewing Sarcoma | 1 | 1 | 0 |
| Osteosarcoma | 1 | 1 | 0 |
| Breast Mass | 1 | 1 | 0 |
| Facial Mass | 1 | 1 | 0 |
| Chondroid Tumor | 1 | 1 | 0 |
| Other Tumors | 9 | 9 | 0 |
| Other Conditions | 6 | 6 | 0 |
Supplemental Table 11. Amplifications and Deletions at 14q11.2, 20203456-20331146: Gains (amplifications) and Losses (deletions) and no. of cases which had the rearrangement are listed by diagnosis
| DX | No. Cases | No. Gain | No. Loss |
| ALL | 3 | 1 | 2 |
| Other Leukemia | 2 | 0 | 2 |
| Osteosarcoma | 1 | 0 | 1 |
| Neuroblastoma | 2 | 0 | 2 |
| Lymphoma | 2 | 0 | 2 |
| MPN | 1 | 1 | 0 |
| Liposarcoma | 1 | 0 | 1 |
| Rectal Polyp | 1 | 0 | 1 |
| Melanoma | 1 | 0 | 1 |
| Other Tumors | 5 | 2 | 3 |
| Other Conditions | 4 | 0 | 4 |