Haplotyping results and number of spanning reads for D4Z4 alleles from FSHD, BAMS, and control fibroblasts, from whole-genome and Cas9-targeted Nanopore sequencing
| 4q | 10q | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| SAMPLE | Haplotype | No. RUsa | No. of WGS spanning reads | No. of Cas9 spanning reads | Upstream D4S2463b | Haplotype | No. RUs | No. of WGS spanning reads | No. of Cas9 spanning reads |
| Control | |||||||||
| AG09309 | 4qBc | ≥38c | 0 | –d | N | 10qA | 10 | 2 | – |
| N/Ae | N/A | 0 | – | N/A | 10qA | 21 | 1 | – | |
| AG10803 | 4qB | 18 | 2 | – | Y | 10qA | 10 | 2 | – |
| 4qB | ≥35 | 0 | – | N | 10qA | 13 | 2 | – | |
| FSHD1 | |||||||||
| 12,566 | 4qAS | 3 | 4 | 20 | Y | 10qA | 9 | 4 | 12 |
| 4qAS | 42 | 1 | 0 | N | 10qB | 19 | 2 | 0 | |
| FSHD1_3 | 4qAL | 1 | 3 | – | Y | 10qA | 15 + 2 + 5f | 1 + 1 + 2g | – |
| 4qB | 17 | 2 | – | Y | 10qA | 35 | 1 | – | |
| 17,706 | 4qAL | 1 | 0 | 53 | N | 10qA | 6 | 4 | 139 |
| 4qAL | 15 | 1 | 80 | Y | 10qA | 14 | 6 | 115 | |
| 4qAL | 40 | 0 | 12 | N | |||||
| 19,187 | 4qAS | 2 | – | 118 | – | 10qA | 15 | – | 33 |
| 4qAS | 22 | – | 6 | – | 10qA | 26 + 1f | – | 12 | |
| 4qAM | 32 | – | 8 | – | |||||
| FSHD2 | |||||||||
| 15,166 | 4qAS | 12 | 4 | – | N | 10qB | 13 | 2 | – |
| 4qB | 21 | 2 | – | N | N/A | N/A | 0 | – | |
| 34,140h | 4qAS | 25 | 1 | – | Y | 10qB | 17 | 3 | – |
| 4qALc | ≥20c | 0 | – | N | 10qA | 19 | 3 | – | |
| 11,491 | 4qAL | 22 | 1 | – | N | 10qA | 6 | 1 | – |
| N/A | N/A | 0 | – | N/A | 10qA | 7 | 1 | – | |
| 11,440 | 4qAS | 11 | – | 14 | – | 10qA | 14 | – | 3 |
| 4qAS | 34 | – | 4 | – | 10qA | 19 | – | 4 | |
| BAMS | |||||||||
| BAMS-1 | 4qAM | 32 | 0 | – | N | 10qA | 12 | 0 | – |
| 4qAS | 47 | 0 | – | N | 10qA | 23 | 3 | – | |
| BAMS-9 | 4qB | 13 | 5 | 100 | Y | 10qA | 7 | 1 | 192 |
| 4qB | 26 | 2 | 27 | Y | 10qA | 31 | 1 | 9 | |
[i] aRefers to the number of complete 3.3 kb KpnI-KpnI D4Z4 units (excluding partial D4Z4 units at the proximal and distal ends).
[ii] bRefers to whether D4S2463, an inverted and truncated D4Z4 unit found ∼42 kb upstream of 4q D4Z4 arrays, is captured in spanning reads from the WGS data.
[iii] cAlleles for which no spanning reads were captured, but whose haplotypes and minimum numbers of repeats were able to be determined from nonspanning reads covering the distal end of the array.
[iv] dDashes (–) indicate that no WGS/Cas9-targeted sequencing was performed for that sample.
[v] e“N/A” indicates alleles whose haplotypes and repeat numbers could not be determined due to the absence of spanning reads or unique nonspanning reads.
[vi] fAlleles with in-cis duplications/triplications of the D4Z4 array.
[vii] gNumber of reads for the triplication allele spanning 1, 2, and all 3 of the arrays, respectively.
[viii] hPreviously diagnosed as FSHD2 based on clinical findings and absence of a contracted D4Z4 array.