Optical genome mapping enables accurate testing of large repeat expansions

Table 1.

Sample and analysis overview

SOC Manual de novo assembly Local guided assembly Molecule distance script
Sample ID Sample material Allele 1 Allele 2 Conclusion Allele 1 Allele 2 Conclusion Allele 1 Allele 2 Conclusion Somatic instability
CNBP_01 EDTA blood >75 18 Detected 3681 20 Detected 61 0 –
CNBP_02 EDTA blood >75 15 Detected 6331 39 Detected 5000 10 Detected A + B
CNBP_03 EDTA blood >75 13 Detected 6517 53 Detected 3659 23 Detected A + B
CNBP_04 EDTA blood >75 15 Detected 7155 −27 Detected 4401 4 Detected A + B
CNBP_05 EDTA blood >75 15 Detected 8042 0 Detected 3521 33 Detected A + B
CNBP_06 EDTA blood >75 15 Detected −14 −15 3687 21 Detected A + B
CNBP_07 EDTA blood >75 16 Detected 5212 −12 Detected 5000 10 Detected A + B
CNBP_08 EDTA blood >75 17 Detected 2502 2 Detected 2661 12 Detected A + B
CNBP_10 EDTA blood >75 13 Detected 2874 −20 Detected 2963 11 Detected A + B
CNBP_11 EDTA blood >75 16 Detected 375 11 Detected 254 34 Detected A + B
CNBP_12 EDTA blood >75 Normal Detected 3471 −16 Detected 3346 14 Detected A
CNBP_13 EDTA blood >75 16 Detected 4634 −14 Detected 4330 3 Detected A + B
CNBP_14 EDTA blood >75 16 Detected 5244 −2 Detected 4186 49 Detected A + B
CNBP_15 EDTA blood >75 Normal Detected 2183 −1 Detected 2092 18 Detected A + B
CNBP_16 EDTA blood >75 Normal Detected 3221 320 Detected 3201 0 Detected A + B
CNBP_17 EDTA blood >75 9 Detected 6275 −13 Detected 5000 2 Detected A + B
CNBP_18 EDTA blood >75 15 Detected 1915 −29 Detected 1656 15 Detected A + B
CNBP_19 EDTA blood >75 Normal Detected 1460 −2 Detected 1574 0 Detected A + B
CNBP_20 EDTA blood >75 Normal Detected 3977 −7 Detected 3577 11 Detected A + B
CNBP_21 EDTA blood >75 18 Detected 288 30 Detected 244 8 Detected A + B
CNBP_22 EDTA blood >75 17 Detected 1683 −24 Detected 1725 70 Detected A + B
CNBP_23 EDTA blood >75 12 Detected 2131 −25 Detected 2515 8 Detected A + B
CNBP_24 EDTA blood 134 Normal Detected −13 −14 3618 10 Detected A + B
CNBP_25 EDTA blood >75 Normal Detected 1476 −19 Detected 2626 9 Detected A + B
CNBP_26 EDTA blood >135 Normal Detected 3737 14 Detected 3241 45 Detected A + B
DMPK_01 EDTA blood >150 11 Detected 269 55 Detected 247 35 Detected –
DMPK_02 EDTA blood >150 11 Detected 456 47 Detected 473 30 Detected –
DMPK_03 EDTA blood >150 5 Detected 252 57 Detected 116 Detected –
DMPK_04 EDTA blood 61 11 Detected 66 66 Detected 60 27 Detected B
DMPK_05 EDTA blood >150 5 Detected 457 54 Detected 485 30 Detected A + B
DMPK_06 EDTA blood 127 5 Detected 64 64 Detected 82 81 Detected B
DMPK_07 EDTA blood >150 12 Detected 378 28 Detected 358 20 Detected –
DMPK_08 EDTA blood 91 5 Detected 67 67 Detected 49 B
DMPK_09 EDTA blood 96–130 5 Detected 71 71 Detected 68 Detected –
DMPK_10 Cell pellet >150 12 Detected 2829 37 Detected 2825 12 Detected A + B
DMPK_11 Cell pellet >150 5 Detected 233 58 Detected 231 12 Detected A + B
DMPK_12 Cell pellet >150 13 Detected 213 24 Detected 219 34 Detected B
DMPK_13 Cell pellet >150 13 Detected 163 21 Detected 167 33 Detected A + B
DMPK_14 Cell pellet >150 13 Detected 202 10 Detected 188 7 Detected B
DMPK_15 Cell pellet >150 6 Detected 1839 28 Detected 1768 53 Detected A + B
DMPK_16 EDTA blood >150 12 Detected 85 85 Detected 52 Detected B
DMPK_17 EDTA blood >150 5 Detected 491 41 Detected 510 15 Detected A + B
DMPK_18 EDTA blood >150 5 Detected 71 71 Detected 69 Detected B
DMPK_19 EDTA blood 73 12 Detected 54 54 Detected 61 0 Detected B
DMPK_20 EDTA blood >150 5 Detected 55 55 Detected 41 B
DMPK_21 EDTA blood >150 12 Detected 1366 43 Detected 1347 23 Detected B
DMPK_22 EDTA blood 74 13 Detected 31 31 61 6 Detected A + B
DMPK_23 EDTA blood >150 7 Detected 372 17 Detected 369 25 Detected A + B
DMPK_24 EDTA blood 130 5 Detected 82 82 Detected 93 78 Detected A + B
DMPK_25 EDTA blood 159 5 Detected 79 79 Detected 109 63 Detected B
DMPK_26 EDTA blood 88 13 Detected 45 45 29 0 A
DMPK_27 EDTA blood >150 5 Detected 1648 21 Detected 20 12 B
DMPK_28 EDTA blood >150 14 Detected 440 41 Detected 393 3 Detected B
DMPK_29 EDTA blood >150 12 Detected 320 20 Detected 310 12 Detected B
DMPK_30 EDTA blood >150 29 Detected 290 63 Detected 131 Detected B
RFC1_01 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1487 1174 Biallelic 1497 1160 Biallelic A
RFC1_02 EDTA blood ≫AAGGG ≫AAAGG Biallelic 738 452 Biallelic 751 458 Biallelic –
RFC1_03 EDTA blood ≫AAGGG ≫AAAAG Biallelic 883 111 Biallelic 897 126 Biallelic A
RFC1_04 EDTA blood ≫AAGGG ≫AAAAG Biallelic 750 97 Biallelic 760 99 Biallelic –
RFC1_05 EDTA blood ≫AAGGG 11 AAAAG Monoallelic 1167 −5 Monoallelic 1175 4 Monoallelic A + B
RFC1_06 EDTA blood ≫AAAAG ≫AAAAG Homozygous 1565 1278 Biallelic 1579 1283 Biallelic A
RFC1_07 EDTA blood ≫AAGGG 11 AAAAG Monoallelic 625 −3 Monoallelic 643 10 Monoallelic –
RFC1_08 EDTA blood ≫AAGGG ≫AAGGG Homozygous 840 840 Homozygous 856 856 Homozygous –
RFC1_09 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1506 770 Biallelic 1499 778 Biallelic A
RFC1_10 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1289 1175 Biallelic 1307 1131 Biallelic A
RFC1_11 EDTA blood ≫AAGGG ≫AAGGG Homozygous 812 812 Homozygous 818 818 Homozygous –
RFC1_12 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1106 895 Biallelic 1121 888 Biallelic A
RFC1_13 EDTA blood ≫AAGGG ≫AAGGG Homozygous 927 927 Homozygous 933 933 Homozygous –
RFC1_14 EDTA blood ≫AAGGG ≫AAGGG Homozygous 725 725 Homozygous 740 737 Biallelic –
RFC1_15 EDTA blood ≫AAGGG ≫AAGGG Homozygous 873 811 Biallelic 887 783 Biallelic A
RFC1_16 EDTA blood ≫AAGGG 11 AAAAG Monoallelic 1104 −11 Monoallelic 1097 4 Monoallelic A + B
RFC1_17 EDTA blood ≫AAGGG 9 AAAAG Monoallelic 711 −1 Monoallelic 723 8 Monoallelic B
RFC1_18 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1444 1134 Biallelic 1474 1127 Biallelic A + B
RFC1_19 EDTA blood ≫AAGGG ≫AAGGG Homozygous 223 40 Biallelic 235 51 Biallelic A
RFC1_20 EDTA blood ≫AAGGG ≫AAAAG Biallelic 494 100 Biallelic 502 106 Biallelic –
RFC1_21 EDTA blood ≫AAGGG ≫AAGGG Homozygous 703 600 Biallelic 715 600 Biallelic A + B
RFC1_22 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1161 905 Biallelic 1180 911 Biallelic A
RFC1_23 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1028 701 Biallelic 1054 733 Biallelic –
RFC1_24 EDTA blood ≫AAGGG 11 AAAAG Monoallelic 602 2 Monoallelic 615 11 Monoallelic A
RFC1_25 EDTA blood ≫AAGGG ≫AAGGG Homozygous 855 854 Biallelic 868 868 Homozygous –
RFC1_26 EDTA blood ≫AAGGG ≫AAGGG Homozygous 714 573 Biallelic 734 585 Biallelic –
RFC1_27 EDTA blood ≫AAGGG ≫AAGGG Homozygous 973 973 Homozygous 987 403 Biallelic A
RFC1_28 EDTA blood ≫AAGGG ≫AAGGG Homozygous 875 875 Homozygous 893 893 Homozygous –
RFC1_29 EDTA blood ≫AAGGG ≫AAGGG Homozygous 1071 890 Biallelic 1073 905 Biallelic –
RFC1_30 EDTA blood ≫AAGGG ≫AAAAG Biallelic 743 74 Biallelic 754 85 Biallelic A

  • For each sample, this table presents the SOC result, as well as the repeat size estimates from the two OGM sizing workflows in repeat units (manual de novo assembly and local guided assembly) and the somatic instability assessment from the molecule distance script workflow. For CNBP and DMPK, the table indicates whether the dominant repeat allele was detected (Detected). For RFC1, we also checked whether OGM identified a monoallelic, biallelic, or homozygous repeat expansion. For the molecule distance script, “A” denotes multiple consensus maps, and “B” denotes a gradient in the molecule distances. We considered somatic instability in cases where both “A + B” provided suggestive evidence.

This Article

  1. Published in Advance March 20, 2025, doi: 10.1101/gr.279491.124 Genome Res. 35: 810-823

Preprint Server



Current Issue

  1. February 2026, 36 (2)
  1. Current Issue
  1. Alert me to new issues of Genome Research