Burt, Randall

Done, Michelle W

Neklason, Deborah

Tuohy, Thérèse

Hereditary Cancer in Clinical Practice

English

PubMed

Michelle W Done

Deborah Neklason

Randall Burt

Thérèse Tuohy

Springer - Publisher Connector

ORAL PRESENTATION Open Access
Shortcuts to genetic characterization of polyposis
patients in a high-risk registry
Michelle W Done1*, Deborah Neklason1,2, Randall Burt1,3, Thérèse Tuohy1
From 14th Annual Meeting of the Collaborative Group of the Americas on Inherited Colorectal Cancer
Dallas, TX, USA. 12-13 October 2010
Background
Mutations in the APC gene lead to Familial adenoma-
tous polyposis (FAP) and an attenuated form of this
condition (AFAP). Mutation detection fails using DNA-
based technology in 20% of FAP and 50% of AFAP
patients due to testing limitations, inability to determine
significance of change, or other responsible genes.
A testing protocol in our Hereditary Gastrointestinal
Cancer Registry has been developed as a research tool
in uncharacterized cases to rule out the obvious APC
mutations, using a multi-step approach. This approach
offers a significant cost savings which could be applied
to clinical genetic testing approaches.
Methods
FAP and AFAP cases were identified through Huntsman
Cancer Institute’s Hereditary Gastrointestinal Cancer
Registry. Participants were first genotyped using 4
genetic markers with high heterozygosity at the APC
locus, spanning 2.8 Mbp. This determines if the patient
may have a common ancestry with families that have
known mutations. When a match was found, follow-up
site-specific testing was done to confirm the known
mutation. Next, two different genetic tests were applied
to rule out common mutations in APC. The hotspot in
APC exon 15, which accounts for 15% of APC muta-
tions, was sequenced for detection of mutations between
(c.3018 and c.4130). The c.426_427delAT founder muta-
tion was evaluated through a high resolution melt-curve
analysis of PCR products. CLIA- and research-negative
cases were then run through an RNA-based assay that
encompasses all of the APC intron/exon boundaries, to
detect mutations that would not be found through cur-
rent clinical testing methods.
Results
Genetic markers were run on individuals from 154 kin-
dreds, resulting in 1680 potential matches at one or
both alleles at each of the 4 genetic markers. Initial ana-
lysis of the data revealed 3 ancestral mutations, and
5 coincident haplotypes; sequence verification is pend-
ing. 120 cases were analyzed for hotspot and founder
mutations; 8 new hotspot and 1 founder cases were
identified. 20 cases were run through RNA analysis, and
2 novel splice defects were identified. Cost analysis was
run on this approach, and we find that the average cost
is $500 versus $2500 for direct sequencing.
Conclusions
This tiered protocol has the advantage of considerable
financial savings and comprehensive evaluation of
genetic changes over current clinical genetic testing
approaches. The protocol is also useful for identification
and expansion of missing branches of those kindreds
currently enrolled in research studies and clinical trials.
Author details
1Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
2Department of Oncological Sciences, University of Utah, Salt Lake City, UT,
USA. 3Department of Medicine, University of Utah, Salt Lake City, UT, USA.
Published: 10 March 2011
doi:10.1186/1897-4287-9-S1-O8
Cite this article as: Done et al.: Shortcuts to genetic characterization of
polyposis patients in a high-risk registry. Hereditary Cancer in Clinical
Practice 2011 9(Suppl 1):O8.
* Correspondence: michelle.condie-done@hci.utah.edu
1Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
Full list of author information is available at the end of the article
Done et al. Hereditary Cancer in Clinical Practice 2011, 9(Suppl 1):O8
http://www.hccpjournal.com/content/9/S1/O8
© 2011 Done et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.


Shortcuts to genetic characterization of polyposis patients in a high-risk registry

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Shortcuts to genetic characterization of polyposis patients in a high-risk registry

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