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Table 1 BRCA1 isoforms identified by long-range PCR and nanopore sequencing

From: Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events

Isoform designation

RNA

Size of isoform (bp)

Number of MinION reads

In-frame/out-of-frame

Deleted protein domain(s)a

Previously described by Colombo et al. [9]b

Δ11q

r.788_4096del

3898

31

In-frame

–

Yes

Δ9,10,11q

r.548_670del + r.788_4096del

3775

27

In-frame

–

Yes

Full length

–

7207

17

In-frame

–

Yes

Δ10-17

r.594_5074del

2726

14

Out-of-frame

BCRT

No

Δ9,11q

r.548_593del + r.788_4096del

3852

10

Out-of-frame

–

Yes

11Δ3110

r.788_3897del

4093

8

In-frame

–

Yes

Δ1Aq,9,10,11q,12-15,16p

r.-25_-20del + r.548_670del + r.788_4804

3061

7

In-frame

–

No

Δ14

r.4358_4484del

7080

6

Out-of-frame

–

Yes

Δ10,11,17

r.594_ 4096del + r.4987_5074del

3616

5

In-frame

BCRT

No

Δ1Aq,11Δ3110,Δ14p,15-17

r.-25_-20del + r.788_3897del + r.4358_4360del + r.4485_ 5074del

3498

5

Out-of-frame

BCRT

No

Δ9,10

r.548_670del

7084

5

In-frame

–

Yes

Δ1Aq,5q,11q,14,21

r.-25_-20del + r.191_212del + r.788_4096del + r.4358_4484del + r.5278_5332del

3688

5

Out-of-frame

RING

No

Δ3

r.81_134del

7153

5

Out-of-frame

RING

Yes

Δ9,10,14

r.548_670del + r.4358_4484del

6957

3

Out-of-frame

–

No

Δ3-23

r.81_ 5467del

1820

3

Out-of-frame

RING, BCRT

No

Δ2,9,10,11q,▼21

r.-19_80del + r.548_670del + r.788_4096del + r.74421_74422ins74421 + 873_74421 + 1001

3676

3

Out-of-frame (loss of coding start site)

RING

No

Δ9-11

r.548_4096del

3658

3

In-frame

–

Yes

Δ2,9,10,11Δ3110,Δ14,20,22

r.-19_80del + r.548_670del + r.788_3897del + r.4358_4484del + r.5194_5277del + r.5333_5406del

3586

3

Out-of-frame (loss of coding start site)

RING, BCRT

No

Δ11q,21

r.788_4096del + r.5278_5332del

3843

3

Out-of-frame

BCRT

No

Δ11

r.671_4096del

3781

2

In-frame

–

Yes

Δ3,11Δ3110

r.81_134del + r.788_3897del

4039

1

Out-of-frame

RING

No

Δ9,10,21

r.548_670del + r.5278_5332del

7029

1

Out-of-frame

BCRT

No

Δ21

r.5278_5332del

7152

1

Out-of-frame

BCRT

Yes

Δ3,9,10,11q

r.81_134del + r.548_670del + r.788_4096del

3721

1

Out-of-frame

RING

No

Δ15-17

r.4485_ 5074del

6617

1

Out-of-frame

BCRT

Yes

11Δ3110,14,20-22

r.788_3897del + r.4358_4484del + r.5194_ 5406del

3753

1

Out-of-frame

BCRT

No

Δ8,11

r.442_547 + r.671_4096del

3675

1

Out-of-frame

–

No

11Δ3110,Δ14

r.788_3897del + r.4358_4484del

3966

1

Out-of-frame

–

No

Δ11q,19,20

r.788_4096del + r.5153_5193_ + r.5194_5277del

3773

1

Out-of-frame

BCRT

No

Δ5,9,10,11q

r.135 _212del + r.548_670del + r.788_4096del

3697

1

In-frame

RING

No

Δ3,9

r.81_134del + r.548_593del

7107

1

Out-of-frame

RING

No

11Δ3110,Δ21,23

r.788_3897del + r.5278_5332del + r.5407_5467del

3977

1

Out-of-frame

BCRT

No

  1. bp base pairs, BRCT BRCA1 C-terminal domain, RING RING finger domain, Δ whole or partial exon skipping, ▼ partial intron retention
  2. aOnly clinically important BRCA1 protein domains are shown (ENIGMA BRCA1/2 Gene Variant Classification Criteria, Version 2.5 29 June 2017, https://enigmaconsortium.org/library/general-documents/). Position of amino acid residues denoting BRCA1 protein domains are as follows: RING, 1–101 and BCRT, 1651–1863
  3. bNovel isoforms that are created entirely from previously identified partial or whole exon skipping events are shown in bold
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Breast Cancer Research

ISSN: 1465-542X

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