22q11.2 LCR rearrangement loci (RL) at nucleotide resolution
| Family (deletion) | Sequencing technology | RL | Nucleotide-level rearrangement locus (hg38) | Gene content | Repeat content |
|---|---|---|---|---|---|
| AD004 (LCR22-A/D) | SLR, ULR, HDR (ONT) | RL-AD1 (160 kb) | 319 bp Chr 22:18,775,948–18,776,026 (A) Chr 22:21,210,278–21,210,356 (D) |
intronic: GGT3P (A) GGT2 (D) |
L2 LINE |
| AD007 (LCR22-A/D) | SLR (ONT) | RL-AD1 (160 kb) | 421 bp Chr 22:18,791,335–18,791,756 (A) Chr 22:21,225,667–21,226,088 (D) |
exonic/intronic: GGT3P (A) GGT2 (D) |
L2 LINE |
| AD008 (LCR22-A/D) | ULR (ONT) | RL-AD1 (160 kb) | 650 bp Chr 22:18,791,386–18,792,037 (A) Chr 22:21,225,716–21,226,367 (D) |
exonic/intronic: GGT3P (A) GGT2 (D) |
L2 LINE |
| AB001 (LCR22-A/B) | ULR (ONT) | RL-B2 (8 kb) | AT repeat within 8 kb locus Chr 22:18,201,246–18,207,385 (A) Chr 22:20,336,265–20,339,445 (D) |
intronic: FAM230D (A) FAM230G (B) |
PATRR |
| AB002 (LCR22-A/B) | ULR (ONT) | RL-B2 (8 kb) | AT repeat within 8 kb locus Chr 22:18,201,246–18,207,385 (A) Chr 22:20,336,265–20,339,445 (D) |
intronic: FAM230D (A) FAM230G (B) |
PATRR |
| AB004 (LCR22-A/B) | Long-range PCR and PacBio SMRT sequencing | RL-B2 (8 kb) | AT repeat within 8 kb locus Chr 22:18,201,246–18,207,385 (A) Chr 22:20,336,265–20,339,445 (D) |
intronic: FAM230D (A) FAM230G (B) |
PATRR |
| AC001 (LCR22-A/C) | ULR (ONT) | RL-C (10 kb) | 119 bp Chr 22:18,855,275–18,855,394 (A) Chr 22:20,698,426–20,698,545 (C) |
– | AluJo SINE |
| AC002 (LCR22-A/C) | ULR (ONT) | RL-C (10 kb) | 866 bp Chr 22:18,845,968–18,846,834 (A) Chr 22:20,689,067–20,689,933 (C) |
exonic: POM121L15P (A) POM121L4P (D) |
AluS SINE |
| BD001 (LCR22-B/D) | STR, ULR (ONT) | RL-B1 (20 kb) | 200 bp Chr 22:18,187,091–18,187,290 (A) Chr 22:20,353,454–20,353,653 (B) |
intronic: FAM230D (A) FAM230G (B) |
/ |
| CD001 (LCR22-C/D) | STR, ULR (ONT) | RL-C (10 kb) | 200 bp Chr 22:20,697,310–20,697,507 (C) Chr 22:21,290,100–21,290,300 (D) |
intronic: POM121L8P (D) | / |
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The first column shows the family identifier, based on Supplemental Table1, and diagnosed deletion type. The fiber-FISH based (Table 1) as well as the length of the RL is presented in the second column. The third column provides the position of the last proximal-specific SNP and the first distal-specific SNP and the length of the locus. The exact position could not be mapped for the three PATRR-mediated LCR22-A/B deletions due to the presence of several PATRRs in the reference genome. Columns four and five show the gene and repeat content, respectively. Repetitive elements and gene exons/introns can be fully or partly covered in the recombination locus. More information on the exact composition of the recombination locus can be found in Supplemental Fig 3. In family BD001, the deletion is diagnosed as LCR22-B/D; however, the recombination occurred between LCR22-A and -B (corresponding to chromosomal loci in the third column), as explained in Figure 4C.
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(RL) Recombination locus, (SLR) standard long-read sequencing, (ULR) ultra-long-read sequencing, (HDR) high duplex read sequencing.
