Open Access Highly Accessed Methodology article

Automated DNA mutation detection using universal conditions direct sequencing: application to ten muscular dystrophy genes

Richard R Bennett1*, Hal E Schneider1, Elicia Estrella1, Stephanie Burgess1, Andrew S Cheng2, Caitlin Barrett1, Va Lip2, Poh San Lai3, Yiping Shen2, Bai-Lin Wu2, Basil T Darras4, Alan H Beggs15 and Louis M Kunkel167

Author Affiliations

1 Program in Genomics and Division of Genetics, and The Manton Center for Orphan Disease Research, Children's Hospital Boston, Boston, Massachusetts, USA

2 Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, USA, and Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA

3 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

4 Department of Neurology, Children's Hospital Boston, Boston, Massachusetts, USA

5 Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA

6 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

7 Howard Hughes Medical Institute, Children's Hospital Boston, Boston, Massachusetts, USA, and Harvard Medical School, Boston, Massachusetts, USA

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BMC Genetics 2009, 10:66  doi:10.1186/1471-2156-10-66

Published: 18 October 2009

Additional files

Additional file 1:

Alan's table genes. A table of known myopathy causing genes

Format: DOC Size: 85KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 2:

Genetests. Excel file listing testing services available.

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Calpain 3 v3022108. Excel file containing CAPN3 assay numbers and associated sequences

Format: XLS Size: 32KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

DMD ASSAY LIST Yiping. Excel file containing DMD assay numbers and associated sequences

Format: XLS Size: 93KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

LMNA assay coverage. Excel file containing LMNA assay numbers and associated sequences

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

SGCB assay coverage. Excel file containing SGCB assay numbers and associated sequences

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

SGCG assay coverage09.04.08. Excel file containing SGCG assay numbers and associated sequences

Format: XLS Size: 13KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

CAV3 assay list. Excel file containing CAV3 assay numbers and associated sequences

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 9:

FKRP assay list. Excel file containing FKRP assay numbers and associated sequences

Format: XLS Size: 19KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

SGCA assay coverage. Excel file containing SGCA assay numbers and associated sequences

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 11:

SGCD coverage090808. Excel file containing SGCD assay numbers and associated sequences

Format: XLS Size: 15KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 12:

TRIM32 assay coverage2. Excel file containing TRIM32 assay numbers and associated sequences

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 13:

UCDS_DMD. A packaged (condensed) methods file for the Hamilton StarPlus robot that can be imported into the Hamilton MicroLab Star Method editor, for the DMD plate (plate 1). This file must be downloaded and saved (not opened) and then imported into the Microlab STAR Method Editor (Hamilton Company).

Format: PKG Size: 2.4MB Download file

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Additional file 14:

UCDS_QUAD. A packaged (condensed) methods file for the Hamilton StarPlus robot that can be imported into the Hamilton MicroLab Star Method editor, for the Quad plate (plate 2). This file must be downloaded and saved (not opened) and then imported into the Microlab STAR Method Editor (Hamilton Company).

Format: PKG Size: 2.4MB Download file

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Additional file 15:

1116vC-Cav3_Template.pt. SeqScape™ template file for CAV3. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S15.ctf to 1471-2156/10/66/suppl/S15.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 9KB Download file

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Additional file 16:

CAPN#-DB.pt. SeqScape™ template file for CAPN3. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S16.ctf to 1471-2156/10/66/suppl/S16.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 18KB Download file

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Additional file 17:

DMD_RSS000009308V01_3730_01.pt. SeqScape™ template file for DMD. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S17.ctf to 1471-2156/10/66/suppl/S17.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 48KB Download file

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Additional file 18:

FKRP_RSS000009239V01_3730_01.pt. SeqScape™ template file for FKRP. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S18.ctf to 1471-2156/10/66/suppl/S18.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 6KB Download file

Open Data

Additional file 19:

LMNA.pt. SeqScape™ template file for LMNAThis file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S19.ctf to 1471-2156/10/66/suppl/S19.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 13KB Download file

Open Data

Additional file 20:

SGCA_103008.pt. SeqScape™ template file for SGCA. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S20.ctf to 1471-2156/10/66/suppl/S20.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 7KB Download file

Open Data

Additional file 21:

SGCB_aug_0608.pt. SeqScape™ template file for SGCB. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S21.ctf to 1471-2156/10/66/suppl/S21.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 8KB Download file

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Additional file 22:

SGCD1 and D2Copy.pt. SeqScape™ template file for SGCD. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S22.ctf to 1471-2156/10/66/suppl/S22.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 21KB Download file

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Additional file 23:

SGCG-Dick051206.pt. SeqScape™ template file for SGCG. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S23.ctf to 1471-2156/10/66/suppl/S23.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 7KB Download file

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Additional file 24:

TRIM32.pt. SeqScape™ template file for TRIM32. This file must be downloaded and saved (not opened) and the file name must be changed to add .pt at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S24.ctf to 1471-2156/10/66/suppl/S24.pt.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 9KB Download file

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Additional file 25:

UCDSdisply_unk_var_only.ds. SeqScape™ template file for display settings. This file must be downloaded and saved (not opened) and the file name must be changed to add .ds at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S25.ctf to 1471-2156/10/66/suppl/S25.ds.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 1KB Download file

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Additional file 26:

UCDSdmddefaults.ad. SeqScape™ template file for analysis defaults settings. This file must be downloaded and saved (not opened) and the file name must be changed to add .ad at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S26.ctf to 1471-2156/10/66/suppl/S26.ad.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 2KB Download file

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Additional file 27:

UCDSprotocol1.ap. SeqScape™ template file for analysis protocol settings. This file must be downloaded and saved (not opened) and the file name must be changed to add .ap at the end of the file name just before the .ctf extension. For example, change file name from 1471-2156/10/66/suppl/S27.ctf to 1471-2156/10/66/suppl/S27.ap.ctf. The file can then be successfully imported into the SeqScape application (ABI).

Format: CTF Size: 2KB Download file

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Additional file 28:

384 welplate tier 2(plate1-DMD)_layout. Excel file shows the assay locations in DMD plate (plate 1).

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 29:

384 welplate tier 3(Plate2)_layout. Excel file that shows the assay locations in plate 2.

Format: XLS Size: 21KB Download file

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Additional file 30:

384 welplate tier 4 (Plate3)_layout. Excel file that shows the assay locations in plate 3.

Format: XLS Size: 17KB Download file

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Additional file 31:

Plate1_assaysbox_EVENSlayout. Excel file that shows the even DMD assay locations in ScreenMate™ box 1

Format: XLS Size: 14KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 32:

Plate1_assaysbox_ODDSlayout. Excel file that shows the odd DMD assay locations in ScreenMate™ box 2

Format: XLS Size: 14KB Download file

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Additional file 33:

Plate2_assaysbox_layout. Excel file that shows the assay locations in ScreenMate™ box for plate 2

Format: XLS Size: 19KB Download file

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Additional file 34:

Plate3_assaysbox_layout. Excel file that shows the assay locations in ScreenMate™ box for plate 3

Format: XLS Size: 15KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 35:

DMD-conversion384-4x96. Excel file showing where assays from a DMD plate will end up in four 96-well plates when taken out of the 384-well plate by quads.

Format: XLS Size: 78KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 36:

Tips on using SeqScape. Short tutorial on setting up and using SeqScape.

Format: DOC Size: 29KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 37:

DMDT1. Picture of QIAxcel report DMD assays in 96 well plate A1 for two patients and one no template control. (See additional file 35 for key to assay number.)

Format: JPEG Size: 416KB Download file

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Additional file 38:

DMDT2. Picture of QIAxcel report DMD assays in 96 well plate A2 for two patients and one no template control. (See additional file 35 for key to assay number.)

Format: JPEG Size: 430KB Download file

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Additional file 39:

DMDT3. Picture of QIAxcel report DMD assays in 96 well plate B1 for two patients and one no template control. (See additional file 35 for key to assay number.)

Format: JPEG Size: 423KB Download file

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Additional file 40:

DMDT4. Picture of QIAxcel report DMD assays in 96 well plate B2 for two patients and one no template control. (See additional file 35 for key to assay number.)

Format: JPEG Size: 451KB Download file

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Additional file 41:

myopathies background, sequence examples and optimization. Seqscape screenshot figures for two compound heterozygous mutations.

Format: DOC Size: 1MB Download file

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Additional file 42:

How to design Assays. MS Word file describing the process used to design primer assays

Format: DOC Size: 39KB Download file

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Additional file 43:

Automation Equipment Evaluation. List of automated liquid handling system evaluation criteria.

Format: DOC Size: 22KB Download file

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Additional file 44:

Process Flow. Excel file showing a flow diagram of the automated process for the DMD (Plate 1)

Format: XLS Size: 306KB Download file

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Additional file 45:

Process Flow Quad. Excel file showing a flow diagram of the automated process for the Quad (Plate 2 or 3)

Format: XLS Size: 307KB Download file

This file can be viewed with: Microsoft Excel Viewer

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