Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Study Population and Basic Characteristics of TCR Sequences
2.2. TCR Repertoire Diversity in MM Samples from IR-seq and RNA-seq
2.3. Proper Read Filtering and Clonotype Abundances at the Single-Patient Level
2.4. Assessment of TCR Genes from IR-seq and RNA-seq after Read Filtering
2.5. Repertoire Inference Using Random Sampling
3. Discussion
4. Materials and Methods
4.1. Sample Collection and Processing
4.2. RNA Sequencing
4.3. Immunoverse Sequencing
4.4. Data Analysis and TCR Repertoire Extraction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Data Availability
Ethics Statements
References
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Clinical Characteristics | |
---|---|
N = 31 | N (%) |
Sample N | 31 |
Gender | |
Male | 17 (54.8) |
Female | 14 (45.2) |
Median Age (Years) | |
≤65 | 13 (41.9) |
>65 | 18 (58.1) |
Average CD138 (-) rate (range) | 0.75 (0.1–22.4) |
Heavy Chain Isotype | |
lgG | 21 (67.7) |
lgA | 6 (19.4) |
lgM | NA |
lgD | NA |
LCD | 1 (3.2) |
Light Chain Isotype | |
Kappa | 17 (54.8) |
Lambda | 11 (35.5) |
R-ISS | |
I | 8 (25.8) |
II | 16 (51.6) |
III | 7 (22.6) |
Fish Results | |
p53 deletion | 4 (12.9) |
p16 deletion | 3 (9.7) |
lgH rearrangement | 10 (32.3) |
1q trisomy | 9 (29) |
RB1 deletion | 9 (29) |
t (14; 16) | 1 (3.2) |
t (4; 14) | 4 (12.9) |
mm_# | RNA Sequencing Results | Immunoverse Results | |||||
---|---|---|---|---|---|---|---|
STAR Mapped Reads | Total Read Counts | Total Unique Clonotypes | Singleton Reads | Total Read Counts | Total Unique Clonotypes | Singleton Reads | |
MM_1 | 54,357,923 | 820 | 431 | 299 | 4,050,594 | 90,068 | 63,126 |
MM_10 | 48,374,912 | 826 | 504 | 403 | 7,293,770 | 250,572 | 199,844 |
MM_19 | 56,698,751 | 819 | 331 | 250 | 10,073,447 | 275,520 | 252,410 |
MM_29 | 59,981,954 | 85 | 65 | 54 | 7,761,188 | 272,594 | 272,079 |
MM_31 | 51,623,766 | 659 | 331 | 241 | 8,120,860 | 403,438 | 373,784 |
MM_34 | 48,536,509 | 1245 | 809 | 649 | 8,836,571 | 821,579 | 688,017 |
MM_35 | 49,161,059 | 1195 | 883 | 697 | 8,039,194 | 423,108 | 366,790 |
MM_36 | 43,189,398 | 652 | 416 | 323 | 9,918,279 | 555,803 | 521,536 |
MM_37 | 52,095,895 | 827 | 613 | 510 | 6,500,208 | 487,124 | 425,707 |
MM_38 | 49,316,301 | 258 | 165 | 124 | 8,195,923 | 408,764 | 378,106 |
MM_39 | 48,288,693 | 716 | 412 | 338 | 9,833,228 | 431,722 | 396,254 |
MM_4 | 34,559,031 | 615 | 451 | 348 | 8,126,107 | 602,704 | 557,693 |
MM_40 | 45,488,936 | 499 | 289 | 198 | 9,963,987 | 127,280 | 105,512 |
MM_41 | 42,258,878 | 202 | 104 | 71 | 8,761,312 | 90,503 | 86,489 |
MM_42 | 45,563,654 | 340 | 120 | 78 | 7,180,034 | 91,962 | 78,633 |
MM_44 | 53,663,728 | 693 | 470 | 371 | 8,595,247 | 281,018 | 200,700 |
MM_46 | 47,093,079 | 408 | 118 | 72 | 8,958,694 | 360,441 | 348,835 |
MM_47 | 46,913,279 | 477 | 299 | 237 | 10,274,849 | 254,130 | 202,285 |
MM_48 | 45,465,437 | 933 | 403 | 308 | 9,565,796 | 559,857 | 501,017 |
MM_49 | 50,302,951 | 628 | 300 | 215 | 9,402,588 | 416,450 | 381,187 |
MM_5 | 46,521,960 | 248 | 141 | 97 | 7,732,378 | 347,955 | 345,460 |
MM_50 | 41,180,449 | 392 | 304 | 250 | 7,324,348 | 176,306 | 126,269 |
MM_6 | 52,868,514 | 1177 | 879 | 712 | 10,053,037 | 1,007,123 | 866,380 |
MM_61 | 41,841,298 | 136 | 71 | 54 | 4,765,448 | 96,738 | 91,318 |
MM_66 | 37,559,665 | 503 | 346 | 259 | 7,836,149 | 205,940 | 163,488 |
MM_67 | 41,723,673 | 904 | 329 | 213 | 6,478,122 | 129,689 | 99,656 |
MM_68 | 45,666,045 | 495 | 313 | 209 | 9,016,842 | 203,599 | 146,692 |
MM_7 | 57,602,270 | 1273 | 912 | 718 | 9,700,140 | 749,213 | 664,845 |
MM_70 | 36,073,087 | 447 | 267 | 199 | 7,430,562 | 210,866 | 154,254 |
MM_71 | 47,691,240 | 1158 | 591 | 412 | 8,943,282 | 204,495 | 141,742 |
MM_72 | 38,540,649 | 306 | 203 | 156 | 6,900,306 | 135,644 | 114,276 |
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Lee, S.; Song, S.; Yoon, S.-S.; Koh, Y.; Yun, H. Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research. Cancers 2020, 12, 3693. https://doi.org/10.3390/cancers12123693
Lee S, Song S, Yoon S-S, Koh Y, Yun H. Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research. Cancers. 2020; 12(12):3693. https://doi.org/10.3390/cancers12123693
Chicago/Turabian StyleLee, Sungyoung, Seulki Song, Sung-Soo Yoon, Youngil Koh, and Hongseok Yun. 2020. "Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research" Cancers 12, no. 12: 3693. https://doi.org/10.3390/cancers12123693