Table 1.
Summary of nanopore LRS findings.
| Individual | Clinically identified variant | Nanopore LRS results and (ACMG category) | Confirmation or supporting findings |
|---|---|---|---|
| 1441‐1 | No variants identified in DMD |
Identified novel maternally inherited 5.9 Mbp inversion that disrupts DMD exons 3–79 (ACMG: P/LP) |
PCR and Sanger sequencing confirmed 1441‐1 is hemizygous and 1441‐2 (mother) is heterozygous for inversion |
| 1441‐2 | Mother of 1441‐1; asymptomatic | Identified novel 5.9 Mbp inversion that disrupts DMD exons 3–79 (ACMG: P/LP) | PCR and Sanger sequencing confirmed 1441‐2 is heterozygous for inversion |
| 1462‐1 | No variants identified in DMD |
Identified maternally inherited intronic splice variant DMD c.5548+67A>G (ACMG: P) |
Sanger sequencing confirmed 1462‐1 is hemizygous and 1462‐2 (mother) is heterozygous for the DMD splice variant; PCR and Sanger sequencing of RNA from muscle specimen confirmed aberrant splicing |
| 1462‐2 | Mother of 1462–1; asymptomatic |
Identified intronic splice variant DMD c.5548+67A>G (ACMG: P) |
Sanger sequencing confirmed 1462‐2 is heterozygous for the DMD splice variant |
| 1480‐1 | No variants identified in DMD |
Identified intronic splice variant DMD c.5155‐16T>A (ACMG: P) |
Sanger sequencing confirmed 1480‐1 is hemizygous for DMD splice variant; aberrant splicing confirmed via minigene assay |
| 1466‐1 | Duplication of DMD exons 10–26, suspected to be nontandem | Determined duplication including DMD exons 10–26 was in tandem and identified breakpoints (ACMG: VUS) | PCR and Sanger sequencing confirmed 1466‐1 is hemizygous for tandem duplication |
| 120‐1 |
LAMA2 c.2962C>T; p.Gln988Ter (ACMG: P/LP) |
An identified novel heterozygous LAMA2 3463 bp duplication (chr6:129,339,012–129,342,475, hg38) (ACMG: P); confirmed clinical SNV | PCR and Sanger sequencing confirmed maternally inherited SV; LRS confirmed previously reported paternally inherited SNV |
| 1126‐1 |
LAMA2 c.2538‐1G>C; (splice variant) (ACMG: LP) |
Confirmed clinical SNV | NA |
| 1443‐1 | Decreased D4Z4 methylation; no FSHD1 or FSHD2 variants identified |
Confirmed SMCHD1 c.182_183 delGT heterozygous variant (ACMG: LP) |
NA |
| 110‐1 |
ANO5 c.692G>T; (p.Gly231Val) (ACMG: P/LP) |
Confirmed clinical SNV | NA |
| 122‐1 |
CAPN3 c.1505T>C; p.Ile502Thr (ACMG: LP) |
Confirmed clinical SNV | Sanger sequencing results suggest SNV is paternally inherited |
| 125‐1 |
CAPN3 c.640G>A; p.Gly214Arg (ACMG: P/LP) |
Confirmed clinical SNV | Sanger sequencing confirmed SNV is paternally inherited |
In 10 individuals, nanopore LRS identified four previously undetected pathogenic or likely pathogenic variants (shown in bold in families 1441, 1462, 1480, and 120), fully characterized a duplication noted on clinical testing, and confirmed all previously noted pathogenic SNVs. Variants identified in this study (in families 1441, 1462, 1480, 1466, 120, and 1443) were classified according to ACMG criteria; previously identified variants were classified by the reporting laboratory or according to their ClinVar designation. LRS, long‐read sequencing; FSHD, facioscapulohumeral muscular dystrophy; P, pathogenic; LP, likely pathogenic; VUS, variant of unknown significance; SNV, single nucleotide variant.