Ion Research Panels:

Panel Name Research Area Genome Number of amplicons per pool
(# of tubes)
Tags Actions
Ion AmpliSeq™ Noonan Research Panel
Developmental Disorders Human (hg19) Pool1: 136 amplicons
Pool2: 132 amplicons
(2 tubes)
DNA
Community Panel
Review panel Sign in to order

Fixed Panel Results Files

Target Mutations

This file provides a list of the genes associated with each Fixed Panel and contains the following information (listed in COSMIC id order):

  • Gene symbol
  • Accession id
  • COSMIC id
  • CDS Mutation - Change occurred in the nucleotide sequence
  • AA Mutation - Change occurred in the peptide sequence as a result of the mutation
  • Strand (+/-)
  • Coordinates (hg19)
  • Amplicon id – Cancer Panel v2 amplicon id nomenclature has changed to represent a more informative reference to the information about the amplicon. The id is now in the format specifying Panel, Gene, and Number of the amplicon associated with the gene (e.g. CHP_KRAS_1).
  • Insert Sequence
  • Target URL – Links to the COSMIC curated mutations database.

Designed BED file

The designed BED files show the amplified regions of the panel. These files are used for data analysis with the Torrent Variant Caller Plug-In. (See Data Analysis section below)

HotSpot BED file

The HotSpot BED file specifies the regions of known mutations with allele specific information such as the (REF) reference, (OBS) observed, and (ANCHOR) anchor fields. The coordinate after the anchor base is used for matching of indels.* Currently, these BED files are only currently available for analysis with the Cancer Panel v1, Cancer Panel v2, and the Comprehensive Cancer Panel. The Inherited Disease Panel does not have an associated HotSpot file as it is not cancer-research focused (and does not have COSMIC ids).

* Note: To avoid the issue of ambiguous right alignment of indel calling, hotspot BED files are left aligned for optimal performance when used with Torrent Variant Caller.

Data Analysis in Torrent Browser

To run data analysis in the Torrent Browser, first upload both the designed BED and hotspots BED files.

For Torrent Suite Software 4.x and 5.x

Go to the Reference section (in the gear menu drop down list). In the left navigation tabs, click Target Regions, then click Add New Target Regions and upload your file.

TS4 Refs

For hotspots, in the left navigation tabs, click Hotspots, then click Add Hotspots and upload your file.

The plan.json file for the Ion AmpliSeq Exome Hi-Q panel has been improved to include updated parameters compatible with Torrent Suite 5.2. These new parameters seek to improve our variant calling performance when using the Hi-Q enzyme with the Ion AmpliSeq Exome panel on the P1 and 540 chips. As part of the update, 4 new parameter.json files have been added to the download zip file to support backwards compatibility with previous versions of Torrent Suite such as 4.6 and 5.0 in a modularized way.

For Torrent Suite Software 3.x

Go to the Reference section (in the gear menu drop down list), and click on hg19. Under the Available BED Files section, click the Upload BED files button. Check the box to indicate it is a HotSpot file.

BED Upload

BED Available

Next

Once the BED files have been successfully uploaded to the Torrent Browser, these files appear in the drop-down menus when running the Torrent Variant Caller. Select the Ion AmpliSeq option in the Library Type:

Variant Caller Plugin

Select your Target Regions and Hotspot Regions BED files from the drop-down menus:

Variant Caller Plugin

* The designer currently only works for Human Reference Genome, hg19.

Summary: Noonan syndrome is a relatively common autosomal dominant congenital disorder. The noonan Panel assesses 14 genes known to be related with this disorder: A2ML1, BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1 and SPRED1. This panel contains 268 amplicons in 2 pools.

Noonan syndrome is a relatively common autosomal dominant congenital disorder with a high phenotypic variability. It is a clinically and genetically heterogeneous disorder that belongs to the group of Rasopathy diseases, caused by mutations in genes dysregulating the RAS/MAPK pathway. The Noonan Research Gene Panel has been developed in collaboration with an European consortia composed by Marco Tartaglia(1), Jose Luis Costa (2), Kornelia Neveling and Marcel Nelen (3) . 1) Istituto Superiore di Sanità, Rome, Italy, 2) Ipatimup, Porto 3) Human Genetics, Radboud UMC Nijmegen . The panel assesses 14 genes known to be related with this disorder. A2ML1, BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1, SPRED1. In a first study of 60 archived samples we showed that very high sensitivity and specificity are achievable. For further details see ASHG 2014 poster “Development and verification of a Noonan genes Ion AmpliSeq™ panel” M. Nelen et al.

Design Date Publication: ASHG 2014 Poster "Development and verification of a Noonan genes Ion AmpliSeq™ panel"
Author: Marcel Nelen (Marcel.Nelen@radboudumc.nl)
Affiliation: Dept. of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
Recommended Application Germ line mutation detection Recommended Configuration Sample per Chip: 8 per 318 chip
Minimum coverage: 684
Sample Type High molecular weight DNA
Number of sample in Publication 60 samples Observed Performance Panel uniformity: 93.05%
Reads on-targets: 98.42%
Input DNA required 2 pool
20 ng total
Disease Research Area: Developmental Disorders