WO2002036819A1

WO2002036819A1 - BRCA1 AND hMLH1 GENE PRIMER SEQUENCES AND METHOD FOR TESTING

Info

Publication number: WO2002036819A1
Application number: PCT/IB2000/001607
Authority: WO
Inventors: Jan Vijg
Original assignee: The Academy Of Applied Science
Priority date: 2000-11-06
Filing date: 2000-11-06
Publication date: 2002-05-10
Also published as: GB2384858A; WO2002036819A9; AU2001210470A1; GB0310933D0

Abstract

Primer sequences and materials are pre-prepared as test kits for enabling appropriate gene scanning patterns, preferably by two dimensional electrophoresis (TDGS), for use in detecting sequence variations and/or mutations in BRCA1 and hMLH1 genes.

Description

BRCAl AND hMLHl GENE PRIMER SEQUENCES AND METHOD FOR TESf ING

The present application is based upon provisional application 60/084408, filed May 6, 1998, and is directed to methods of and primer sequences for sequence varia- ^" tion and/or mutation detection of BRCA and hMLHl genes , such as by two- dimensional denaturing gradient electrophoresis techniques (TDGS). Background

Such techniques are described in Method Of And Apparatus For Diagnostic DNA Testing, Jan Vijg and Daizong Li, PCT/1B96/00543, filed 3 June 1996, International Publication Number WO96/39535, 12 December 1996, and in "Two-Dimensional DNA Typing", Molecular Bio Technolgoy, Vol. 4, 1995, pp 275-295.

The tests leading to the establishment of the primer sequences for the BRCAl and hMLHl of the present invention were conducted with the TDGS design prepared with the computer programming and equipment described in PCT/IB97/00976, published on or about February 14, 1998. Objects of Invention and Summary

The objects of the invention are to provide novel theoretically and empirically (experimentally) derived TDGS patterns for hMLHl and BRCAl genes which may be . used by testers to test for gene sequence variation and/or mutations. rigs. 1 A and IB show^' the computer-aided design TDGS patterns obtained for the hMLHl and BRCA l (theoretical-left hand side; empirical or experimental—right hand side).

In the theoretical vs. empirical patterns of the MLHI and BRCAl genes, for all four genes; one or more exons were designed in overlapping fragments, in which case the fragment name is exon.1, exon..2, etc. Exons 8 and 15 of hMLHl contain polymorphisms, which can be distinguished from disease-causing heterozygous mutations on the basis of a unique four-spot pattern (18). Description Of The Invention In Preferred Forms

HI DNA mismatch repair gene. The design for MLHI took 30 minutes (excluding lication). Fig. 1A shows the theoretical and the empirical TDGS pattern for the MLHI gene. Because exons 11 and 12 had to subdivided into overlapping fragments, two multiplex groups are currently being used, with the long PCR carried out as a four-plex PCR. Like many other genes, exon 1 of MLHI is GC-rich and, hence, was found to melt at a much higher % UF compared to most of the other fragments. Thus far, a total of 41 coded samples with previously identified mutations have been analyzed in a blinded fashion with 100% concordance (30).

The breast and ovarian cancer susceptibility gene BRCAl. The tumor supressor gene BRCAl contains 24 exons, of which exon 11 contains approximately 60% of the coding region. Fig. IB shows the theoretical and empirical 2-D pattern for BRCAl. Of all 2-D designs discussed, this was the most difficult (total design time was 2 h), the main reason being the need to make overlapping fragments for the 3.4kb exon 11. Pre- amplification was accomplished by one 7-plex long PCR. Using the long PCR amplicons as template, all 24 exons were amplified in a total of 37 fragments distributed over 5 multiplex groups. The overlap and sometimes short distances from fragment to fragment necessitated the use of so many multiplex short PCR groups. The non-coding exons 1 a, 1 b and the non-coding part of exon 24 were excluded. Evaluation of this test design using a panel of coded samples with previously identified mutations is currently ongoing. Thus far, mutations and polymorphisms have been detected in exons 2, 8, 11, 16, 20 and r-plification

Primers were obtained from Genosys Biotechnologies, Inc. (The Woodlands, TX). For complete lists of all sequences, except BRCAl, see references 18, 29 and 30. Primer sequences for BRCAl will be published elsewhere but will be made available upon request. PCR amplification of gene sequences was carried out using the two-step protocol first described by Li and Vijg (22). Primers for long-distance PCR were designed based on published sequences (24-27) using Primer Designer 3, to amplify the entire gene-coding region for each of the 4 genes as a 1-plex (TP53), a 6-plex PCR (RBI), a 4-plex PCR (MLHI) or a 7-plex PCR (BRCAl). The LA PCR kit (Takara) was used for long PCR in a PTC-100 thermocycler (MJ Research). Multiplex short PCR was carried out using the long PCR products as template. Between 0.1 and 1.125 μM of each primer was used in a 50 μl reaction with 1 μl of long PCR product in 20 MM Tris-HCl (pH 8.4), 50 mM KCI, 250 μM of each dNTP and 5% formamide. Two and a half units of Taq DNA polymerase (Life Technologies) were added after an initial denaturation at 94 °C for 60 s.

Cycling conditions for multiplex short PCR and concentrations of MgCl2 varied among

different genes and amplifications were carried out in a PTC-100 thermocycler (MJ Research).

Two-dimensional DNA electrophoresis

For RBI, 5 μl of multiplex short PCR was used per electrophoresis run. For TP53, MLHI and BRCAl, 5 μl of each of the different multiplex groups were combined. One tenth of a of loading buffer (0.25% xylene cyanol, 0.25% bromophenol blue, 15% ficoli and

Na2 EDTA) was added and the mixtures were loaded onto a 6.5% (TP53) or

10% (RBI, MLHI and BRCAl) PAA non-denaturing size gel (acrylamide: bisacrylamide = 37.5:1) in 0.5 xTAE buffer. The samples were electrophoresed for 5.3 h at 150 V (RBI), 5 h at 120 V (TP53) or 7.5 h at 140 V (MLHI and BRCAl) at 50° C. After staining the gel with a mixture of equal amounts of SYBR-green I and II (Molecular Probes, Eugene, Oregon) for 20 min, the region containing all fragments of interest (usually between 100 and 600 bp) was cut out and loaded onto a denaturing gradient gel (DGGE). Gradients used were 0 to 50% UF for RBI, 20 to 70% for TP53, 25 to 70% UF for MLHI and 20 to 65% for BRCAl. The second orthogonal dimension was run for 12 h at 100V (RBI), 14 h at 120V (TP53), or 16 h at 100V (MLHI and BRCAl). Spot patterns were visualised by SYBR-green staining using a Fluorlmager (Molecular Dynamics, Sunnyvale, California).

EQUENCES AND TARGET FRAGMENT LENGTH FOR hMLHl LONG -X PCR

hMLHl 1-4F - SEQ ID NO: 1 hMLHl 1-4R - SEQ ID NO: 2

TARGET FRAGMENT LENGTH: 10.8KB

EXONS 5-10 hMLHl 5-10F - SEQ ID NO: 3 hMLHl 5-10R - SEQ ID NO: 4

TARGET FRAGMENT LENGTH: 10.5KB

EXONS 11-13 hMLHl l l-13F - SEQ ID NO: 5 hMLHl 11-13R - SEQ ID NO: 6

TARGET FRAGMENT LENGTH: 8.7KB

EXONS 14-19 hMLHl 14-19F- SEQ ID NO: 7 hMLHl 14-19R - SEQ ID NO: 8

TARGET FRAGMENT LENGTH: 10.5KB

Table 2

PRIMER SEQUENCES AND TARGET FRAGMENT LENGTH FOR BRCAl LONG MULTIPLEX PCR

EXONS 1-3

PRIMER SEQUENCES BRCAl 1-3F - SEQ ID NO: 33 BRCAl 1-3R - SEQ ID NO: 34

TARGET FRAGMENT SIZE: 9.9KB

EXONS 5-9

PRIMER SEQUENCES BRCAl 5-9F - SEQ ID NO: 35 BRCAl 5-9R - SEQ ID NO: 36

TARGET FRAGMENT SIZE: 9JKB itiπued

11

PRIMER SEQUENCES BRCAl 10-1 IF - SEQ ID NO: 37 BRCAl 10-11R - SEQ ID NO: 38

TARGET FRAGMENT SIZE: 4.8KB

EXONS 12-13

PRIMER SEQUENCES BRCAl 12-13F - SEQ ID NO: 39 BRCAl 12-13R - SEQ ID NO: 40

TARGET FRAGMENT SIZE: 9.0KB

EXONS 14-17

PRIMER SEQUENCES BRCAl 14-17F- SEQ ID NO: 41 BRCAl 14-17R - SEQ ID NO: 42

TARGET FRAGMENT SIZE: 10.7KB

EXONS 18-20

PRIMER SEQUENCES BRCAl 18-20F - SEQ ID NO: 43 BRCAl 18-20R- SEQ ID NO: 44

TARGET FRAGMENT SIZE: 7.2KB

EXONS 21-24

PRIMER SEQUENCES BRCAl 21-24F - SEQ ID NO: 45 BRCAl 21-24R - SEQ ID NO: 46

TARGET FRAGMENT SIZE: 11.4KB

Table 3

Table 3

lontiπued

6819

ntinued

Claims

; claimed is:

1. A method for detecting mutations in the BRA1 and hMLHl genes comprising providing PCR primers capable of amplifying the entire coding sequence of the BRCAl and hMLHl genes; amplifying a test sample containing nucleotide sequences by PCR with these primers producing a first set of amplification products; subjecting this first set of amplification products to short distance multiplex PCR; providing a second set of amplification products using substantially the respective primer pairs of Tables 4 and 1 for this short distance PCR; and subjecting the second set of amplification products to two-dimensional gel electrophoresis to produce a characteristic spot pattern for a specific mutation in either the BRCAl or the hMLHl gene.

2. The method of claim 10 wherein non-denaturing gels and buffer materials are used so as to enable combined mixtures of multiple groups of BRCAl and hMLHl genes to be subjected to the electrophoresis together.

3. Test kits for enabling BRCAl gene testing comprising the short PCR primer pairs listed in Table 4 mixed in about 20mM of Tris-HCl, 50mM KC1, 25μM of d NTP and 5% formamide.

4. The test kits of claim 3 wherein a gel or gel material is also provided comprising acrylamide and bisacrylamide in a ratio of about 37.5 to 1, in a buffer.

5. The test kits of claim 4 wherein the gel or gel material is provided with about 20- 65% of UF (urea and formamide).

6. Test kits for enabling hMLHl gene testing comprising the short PCR primer pairs listed in Table 3 mixed in about 20mM of Tris-HCl, 50mM KCL, 25μM of d NTP and 5% formamide. he test kits of claim 6 wherein a gel is also provided comprising acrylamide icrylamide in a ratio of about 37.5 to 1, in a buffer.

--'he test kits of claim 7 wherein the gel is provided with about 25-75% of UF (urea and formamide).