Table 1.
Haplotype and breakpoint junction features among probands carrying DUP-TRP/INV-DUP
| Patient identifier | BH identifier | Haplotype structure | Jct1/Jct2 single molecule | MECP2 inverted (Y/N) | Junction 1 | Inverted repeat pair | Intra-/interchromosomal event | Junction 2 | Previous studies |
|---|---|---|---|---|---|---|---|---|---|
| BAB2727 | BH16106_1 | ND | ND | ND | PB (ChrX:153,613,143–153,615,342) | 43221a/43221b (K1/K2) | N/A | microhomology 2 bp + templated insertion | Carvalho et al.16 |
| BAB2769 | N/A | 3 | no | no | OGM, Sanger | 43202a/43202b | intrachromosomal | microhomology: 2 bp + deletion | Carvalho et al.5 |
| BAB2772 | N/A | 3 | yes | yes | OGM | 43221a/43221b (K1/K2) | intrachromosomal | Microhomology: 3 bp | Carvalho et al.5 |
| BAB2796 | BH16110_1 | 2 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | 2 bp insertion | Carvalho et al.5 |
| BAB2797 | N/A | ND | ND | ND | ND | 43221a/43221b (K1/K2) | intrachromosomal | 1 bp insertion | Carvalho et al.5 |
| BAB2801 | BH15649_1 | 4 | yes | yes | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 7 bp | Carvalho et al.5 |
| BAB2805 | N/A | ND | ND | yes | ND | 43221a/43221b (K1/K2) | intrachromosomal | blunt junction | Carvalho et al.5 |
| BAB3114 | BH14245_1 | 1 | no | yes | OGM, PB (ChrX:153,613,143–153,615,342) | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 2 bp | Carvalho et al.5 |
| BAB3147 | BH16111_1 | 6 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 2 bp | Carvalho et al.17 |
| BAB3216 | N/A | ND | ND | ND | ND | 43202a/43202b | intrachromosomal | microhomology: 4 bp + templated insertion | Carvalho et al.17 |
| BAB3255 | BH16108_1 | 1 or 3 | no | yes | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 2 bp | Carvalho et al.17 |
| BAB3274 | BH16112_1 | 1 or 3 | no | yes | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 3 bp + 9 bp + 5 bp deletions | Carvalho et al.17 |
| BAB12566 | BH13842_1 | 1 | no | N/A | OGM | 37696a/37696b | interchromosomal | microhomology: 2 bp | This study |
| BAB14392 | BH15645_1 | ND | ND | ND | ND | 43231a/43231b (L1/L2) | intrachromosomal | microhomology: 1 bp | This study |
| BAB14547 | BH15700_1 | 3 | yes | yes | OGM, PB (ChrX:153,613,143–153,615,342) | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 1 bp | This study |
| BAB14604 | BH15701_1 | 3 | yes | yes | OGM, PB (ChrX:153,613,143–153,618,666) | 43221a/43221b (K1/K2) | N/A | microhomology: 1 bp | This study |
| BAB14686 | BH15640_1 | 2 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 2 bp | This study |
| BAB15418 | BH16300_1 | 4 | yes | no | OGM | 43221a/43221b (K1/K2) | N/A | microhomology: 2 bp | This study |
| BAB15428 | BH16301_1 | 1 or 3 or 13 | no | yes | OGM | 43231a/43231b(L1/L2) | interchromosomal | AluY/AluSx1 at breakpoint | This study |
| BAB15702 | BH16609_1 | 6 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 9 bp | This study |
| BAB15705 | BH16611_1 | 2 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 6 bp (AluYa8/AluJo) | This study |
| BAB15740 | BH16610_1 | 2 | yes | no | OGM | 43221a/43221b (K1/K2) | intrachromosomal | microhomology: 2 bp | This study |
| BAB15789 | N/A | 2 | yes | no | OGM | 43221a/43221b (K1/K2) | N/A | microhomology: 2 bp | This study |
| BAB15420 | BH16299_2 | ND | ND | ND | ND | 43221a/43221b (K1/K2) | N/A | complexities | This study |
The majority of patients contain MECP2 in duplicated segment A/A′, except BAB3147, BAB15420 (truncated MECP2 – B/B′); BAB2801, BAB2805, BAB3114, BAB2797 (triplicated MECP2 – B/B′); BAB2769, BAB3216 – C/C′. N/A, not available; ND, not determined; OGM, optical genome mapping; PB, PacBio HiFi.