Table 1.
List of participants included in this study. Comparison of pathogenic 4q35A allele characteristics using SB and OGM as well as details on the specimen stability used in OGM. Optical genome mapping was performed on specimens stored and processed under two representative conditions: 7 days (d) post-collection and subsequent extraction for Indian samples, and 1 day (d) post-collection and subsequent extraction for UK samples. Four additional samples were tested using archived agarose plugs. SB results were compared with those of OGM. N50 (>0.2) is used as a surrogate marker of molecule size; N50 values represent weighted average lengths of DNA molecules that are 20 Kbp or longer. Map rate (%) indicates the percentage of molecules 150 Kbp or longer that map to the reference genome. Effective coverage indicates the total amount of aligned molecules divided by the length of the reference genome multiplied by the map rate. SB-LGE: Southern blot and Linear Gel Electrophoresis; SB-PFGE: Southern blot and Pulsed-Field Gel Electrophoresis; NA; not analysed; ND: not detected, assumed to be >48 Kb; Methylation FSHD2 thresholds: delta1 ≤ 20%.
| Specimen ID # | Source | Methylation | SB-LGE | SB-PFGE | OGM | Shipping/Storing | Molecules ≥ 150 Kbp | N50 > 0.2 | Map Rate (%) | Effective Coverage | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4q_1 | Outcome | 4q_1 | 4q_2 | Outcome | 4q_1 | 4q_2 | Outcome | ||||||||||||
| FseI (delta1) * | U | U | A/B | U | A/B | U | A/B | U | A/B | ||||||||||
| NHNN_FSH001 | UK | NA | >10 | No F1 No F2 | 23 | B | 24 | B | Negative | 23 | B | 24 | B | No F1, No F2 | d1, −80 °C | 332 | 0.277 | 94 | 166× |
| NHNN_FSH002 | UK | NA | 7 | FSHD1 | NA | NA | NA | NA | - | 7 | A | 49 | A | FSHD1 | d1, −80 °C | 304 | 0.248 | 95 | 151× |
| NHNN_FSH003 | UK | NA | 6 | FSHD1 | NA | NA | NA | NA | - | 6 | A | 39 | A | FSHD1 | d1, −80 °C | 382 | 0.340 | 93 | 147× |
| NHNN_FSH004 | UK | NA | 8 | FSHD1 | NA | NA | NA | NA | - | 7 | A | 29 | A | FSHD1 | d1, −80 °C | 242 | 0.186 | 91 | 142× |
| NHNN_FSH005 | UK | NA | >10 | FSHD2 | NA | NA | NA | NA | - | 18 | A | 24 | B | FSHD2 | d1, −80 °C | 293 | 0.228 | 65 | 106× |
| NHNN_FSH006 | UK | NA | 1 | FSHD1 # | NA | NA | NA | NA | - | [1(64%);43(36%)] | A | 26 | B | FSHD1 mosaic | d1, −80 °C | 258 | 0.198 | 91 | 172× |
| NHNN_FSH007 | UK | NA | 5 | FSHD1 | NA | NA | NA | NA | - | 5 | A | 27 | B | FSHD1 | d1, −80 °C | 220 | 0.158 | 88 | 145× |
| NHNN_FSH008 | UK | −13 | 11 | No F1, No F2 | 10 | A | 10 | A | FSHD1 ^ | 10 | A | 10 | A | FSHD1 ^ | d1, −80 °C | 213 | 0.143 | 79 | 122× |
| NHNN_FSH009 | UK | NA | 8 | FSHD1 | NA | NA | NA | NA | - | 7 | A | 18 | A | FSHD1 | d1, −80 °C | 203 | 0.120 | 75 | 83× |
| NHNN_FSH010 | UK | NA | >10 | No F1, No F2 | 13 + 6 | A | 22 | A | FSHD dup | 13 + D | A | 22 | A | FSHD dup | d1, −80 °C | 203 | 0.142 | 83 | 131× |
| IC_AIM_000950 | India | 0 | NA | - | 12 | B | 43 | A | No F1, No F2 | 12 | B | 42 | A | No F1, No F2 | 4 °C, d7, −80 °C | 251 | 0.131 | 80 | 134× |
| IC_AIM_000918 | India | NA | NA | - | 2 | A | 23 | B | FSHD1 | 2 | A | 23 | B | FSHD1 | 4 °C, d7, −80 °C | 237 | 0.126 | 81 | 136× |
| IC_AIM_000955 | India | NA | NA | - | 5 | A | 22 | A | FSHD1 | 4 | A | 22 | A | FSHD1 | 4 °C, d7, −80 °C | 228 | 0.118 | 74 | 105× |
| IC_AIM_000957 | India | NA | NA | - | 5 | A | 39 | A | FSHD1 | 4 | A | 38 | A | FSHD1 | 4 °C, d7, −80 °C | 249 | 0.103 | 77 | 123× |
| IC_AIM_000904 | India | NA | NA | - | 3 | A | 24 | B | FSHD1 | 3 | A | 24 | B | FSHD1 | 4 °C, d7, −80 °C | 220 | 0.094 | 67 | 107× |
| IC_AIM_000963 | India | NA | NA | - | 4 | A | 25 | A | FSHD1 | 4 | A | 25 | A | FSHD1 | 4 °C, d7, −80 °C | 270 | 0.158 | 83 | 132× |
| IC_AIM_000932 | India | −35 | NA | - | 9 | A | 12 | B | FSHD2 | 9 | A | 12 | B | FSHD2 | 4 °C, d7, −80 °C | 236 | 0.105 | 80 | 122× |
| IC_AIM_001042 | India | −41 | NA | - | 19 | A | 19 | A | FSHD2 | 20 | A | 20 | A | FSHD2 | 4 °C, d7, −80 °C | 221 | 0.090 | 38 | 62× |
| IC_AIM_001045 | India | NA | NA | - | 5 | A | 25 | B | FSHD1 | 4 | A | 25 | B | FSHD1 | 4 °C, d7, −80 °C | 213 | 0.100 | 64 | 112× |
| IC_AIM_001053 | India | NA | NA | - | 4 | A | 21 | B | FSHD1 | 3 | A | 21 | B | FSHD1 | 4 °C, d7, −80 °C | 235 | 0.147 | 78 | 123× |
| IC_AIM_001055 | India | NA | NA | - | 6 | A | 25 | A | FSHD1 | 7 | A | >11 | ND | FSHD1 | 4 °C, d7, −80 °C | 185 | 0.083 | 42 | 66× |
| IC_AIM_000820 | India | NA | NA | - | 4 | A | 23 + 6 | AD | FSHD1 | 3 | A | 24 + D | A | FSHD1 | 4 °C, d5 | 212 | 0.161 | 78 | 51× |
| IC_AIM_00152 | India | 16 | NA | - | 28 | A | 59 + 3 | AD | FSHD dup | 26 | A | 61 + D | A | FSHD dup | 4 °C, d5 | 289 | 0.234 | 88 | 102× |
| IC_AIM_000701 | India | NA | NA | - | [2(40%);20(60%)] | A | 10 | B | FSHD1 mosaic | [2(36%);21(64%)] | A | 10 | B | FSHD1 mosaic | 4 °C, d5 | 260 | 0.177 | 80 | 128× |
| IC_AIM_000531 | India | −8 | NA | - | 17 | B | 20 | A | No F1, No F2 | 17 | B | 21 | A | No F1, No F2 | 4 °C, d5 | 250 | 0.167 | 74 | 89× |
* delta1 values represent repeat size-corrected D4Z4 methylation calculated as described in Lemmers et al. 2014 [17]. # mosaicism character of the FSHD1 allele was not identified by SB-LGE in sample NHNN_FSH006. ^ homozygous 10 U. NHNN_FSHD008 has a phenotype consistent with FSHD (facial weakness; shoulder and pelvic girdle weakness) and was found to contain Homozygous 10 U via OGM.