throbber
Case 2:13-cv-00640-RJS Document 103-11 Filed 08/31/13 Page 3 of 6
`!CANCER RESEARCH ~4. 254R- 2S51. May 15, 1'194]
`
`Advances in Brief
`
`Evidence for Involvement of BRCAl in Sporadic Breast Carcinomas
`
`Craig S. Cropp, Heli A. Nevanlinna, Seppo Pyrhonen, Ulf-HAkan Stenman, Paul Salmikangas, Hans Albertsen,
`Ray White, and Robert Callahan
`Laboratory of Tumor l111munology and Biology, National Canur Institute, NIH. Bethesda, MD 20892 [C. C .. R. C.j; Departmeflls I and If of Obstetrics and Gynecology
`[H. A. N .. U·H. S .. P. S.j and Radiotherapy and Oncology {5. P.j, Helsinl<i University Central Hospital, HuartmaninJt.atu 2, 00290 Helsinlti, Finland; and Eccles lnstituJe of
`Human Genetic.< and lloward llughes Medica/Institute, University of Utah, Salt Lou City, Utah 84112/H. A .. R. W.f
`
`describe a high density deletion map using 17 PCR-based polymor(cid:173)
`phic STS markers located between the Dl7S250 and Dl7S579 loci in
`130 primary human breast tumors.
`
`Materials and Metbods
`
`Primary breast carcinomas and matc.bing peripheral lymphocytes were
`collected at the Helsinki University Central Hospital in Helsinki, Finland, from
`130 patients who had received no prior therapy.
`Genomic DNA was extracted and diluted to 100- 200 ng/1Jol. PCR was
`performed with 100- 200 ng template DNA, 10 mM Tris-HCl, 1.5 mM MgCI2>
`50 mM KCI, gelatin 0.1 mglml, 250 IJoM concentration of each nucleoside
`triphosphate, 0.4 unit Taq polymerase (Boehringer Mannheim), and 30 pmol of
`each primer in a total volume of 25 IJo). The PCR product was identified by end
`labeling primers with ['y-32P]ATP. All PCR reactions were performed on a
`GeneAmp PCR System 9600 starting with denaturation for 6 min at 94°C
`followed by 25 cycles of denaturation at 94•c for 10 s, annealing temperature
`for 10 s, and extension at 72"C for 20 s. The primers used, their annealing
`temperatures, and references are shown in Table I.
`The PCR products were diluted with loading buffer (95% formamide, 20
`mM EDTA, 0.05% bromophenol blue, and 0.05% xylene cyanol), beat dena(cid:173)
`tured and rapidly cooled. Samples were run in pairs (tumor and lymphocyte
`PCR product from the same patient) on a denaturing gel (7% acrylamide-32%
`fonnamide-6 M urea-1 X Tris-buffered EDTA) at a constant65-70 W. After
`electrophoresis the gel was transferred to Whatman No. 3MM paper and
`autoradiography was performed with Kodak X-Omat AR film at - 70"C.
`
`Results and Discussion
`
`Abstract
`
`The hereditary brust cancer gene BRCAJ previously has been localized
`to chromosome 17q2l. We looked for evidence of involvement of tbis
`region of chromosome 17 in 130 sporadic breast cancers. Seventeen poly(cid:173)
`morphic sequence tagged site markers were examined in these tumors
`between the Dl7S250 and Dl7S579 loci to screen for deletions as mea(cid:173)
`sured by loss or heterozygosity. The smallest common region that was
`deleted occurred in the approximately 120-ldlobase interval between the
`D17S846 and Dl7S746 loci within the BRCAJ region. Ddineatioo or this
`commonly deleted area should accelerate attempts to identify the involved
`gene(s) and its relationship to BRCA/.
`
`Introduction
`
`It is widely believed that there are one or more tumor suppressor
`genes on chromosome 17q for breast carcinoma (1-3). One candidate
`gene, BRCAJ, is genetically linked to the development of some
`familial breast cancers and is located at 17q21 (4). Ovarian cancer is
`also known to have a hereditary component (5-7). Furthermore, a
`woman with ovarian cancer is at increased risk for developing breast
`cancer as a second primary tumor, and vice versa (8- 10}. Recently,
`the syndrome for familial breast/ovarian cancer has also been linked
`to the same region as BRCAJ (11). The observed LOH 1 affecting the
`wild type chromosome in tumors from affected breast/ovarian cancer
`patients (12, 13) is consistent with the hypothesis that BRCAJ is a
`tumor suppressor gene. However, whether the target genes for familial
`breast and breast/ovarian cancers are the same or are different closely
`linked genes is not known. In a variety of hereditary neoplasias the
`affected gene (e.g., RB, TP53, APC, etc.) has also been found to be
`frequently mutated in sporadic forms of the disease (14, 15). Previ(cid:173)
`ously, we (1} and others {2, 3, 16) have shown that sporadic breast
`carcinomas are frequently affected by LOH in the general region of
`BRCAJ. The availability of additional polymorphic STS which have
`been genetically mapped to the region of chromosome 17q21 con(cid:173)
`taining BRCA 1 (17} has provided us the opportunity to further define
`the region of this portion of the genome which is affected by LOH in
`sporadic primary human breast tumors. When this study was begun
`the consensus among published reports on the genetic and physical
`boundaries of BRCAJ suggested that the centromeric boundary was
`D17S250 (18-20). The telomeric boundary was less clear. In some
`reports it was Dl7S588 while in others it was the more centromeric
`locus, Dl7S579 (19, 21, 22). In our study we chose Dl7S579 as our
`telomeric border. The interval between DJ7S250 and Dl7S579 is
`estimated to be roughly 3500 kilobases (23). In the present study we
`
`We have previously defined three regions of chromosome 17q that
`are frequently affected by LOH in primary human breast tumors (1).
`In that study a putative target gene(s) was suggested in the interval
`between Dl7S73 and NMEJ on chromosome 17q12-q21. In the
`present study we have examined an additional 17 polymorphic STS
`markers between D17S250 and Dl7S579 which is a subregion within
`the D17S73 and NMEI interval. This represents an average of one
`polymorphism every 210 kilobases since the distance between
`D17S250 and Dl7S579 is estimated to be 3500 kilobases. The total
`number of tumors examined, the percentage of the total number of
`tumors that were informative, and the percentage of the informative
`tumors which were deleted (i.e., LOH) is shown in Table 1. The
`overall frequency of LOH varies from 12 to 32% and is the highest
`between Dl7S846 and DJ7S776.
`To further define the region containing the putative target gene we
`have analyzed the genotypes of individual primary breast tumor
`DNAs for evidence of LOH. Shown in Fig. 1 are autoradiographs of
`the STS markers of four breast tumors between D 17S702 and
`D17S856. Tumor 20 showed no LOH at D17S702 and Dl7S746 but
`was deleted for the upper allele of GAS and the lower allele of
`D17S846. Markers Dl7S776 and D17S856 were not informative in
`this tumor. In tumor 26 no LOH was detected at DJ7S702, D17S846,
`and Dl7S856, but the tumor DNA was deleted for the lower allele of
`2548
`
`Received 2/24/94; accepted 4/5/94.
`The costs of publication of this article were defrayed in part by lhe paymenl of page
`charges. This article musl therefore be hereby marked advcrtisrmenr in accordance wilh
`18 U.S.C. Section 1734 solely 10 indicate this fact.
`' The abbreviations used are: LOH. loss of heterozygosity; STS, sequence tag siles;
`PCR, polymerase chain reaction
`
`Downloaded from
`
`cancerres.aacrjournals.org
`
`on August 27, 2013. © 1994 American Association for Cancer
`Research.
`
`GeneDX 1032, pg. 1
`
`

`

`Case 2:13-cv-00640-RJS Document 103-11 Filed 08/31/13 Page 4 of 6
`
`BRCAJ LN SPORADIC BREAST CARCINOMAS
`
`Table I Frequency of LOH at chro1110$ome 17q21 loci
`The locus number of tbe STS marker, the PCR annealing temperature, and a reference
`is listed for each marker used. The total number of tumors e~amined for each marker is
`indicated by N. The percentage of the total number of tumors (N) that were informative
`is shown as %1, and the numbers in parentheses are the expected heterozygosity for that
`STS marker. The percentage of tbe informative tumors (I) that were deleted is indicated
`by %LOH.
`
`LocusiSTS
`
`D/75250
`THRAJ
`Dl7S700
`Dl7S857
`Dl7S702
`GAS
`D/75846
`Dl7S746
`DJ7S776
`Dl7S856
`Dl7S648
`Dl7S855
`Dl7S902
`DI7S859
`D17S750
`Dl7SI83
`Dl7S579
`
`Annealing
`temperature
`(.C)
`
`55
`55
`60
`55
`52
`60
`55
`58
`58
`55
`60
`55
`60
`55
`65
`55
`55
`
`Ref.
`24
`25
`17
`26
`17
`27
`28
`17
`29
`26
`17
`26
`17
`26
`17
`30,31
`32
`
`N
`
`101
`95
`100
`102
`102
`97
`95
`108
`105
`103
`107
`60
`50
`49
`103
`103
`109
`
`%1
`
`80(81)
`39(81)
`54 (44)
`67 (NP)
`90(88)
`52(NP)
`78 (84)
`33 (44)
`60(55)
`51 (NP)
`36(29)
`50(NP)
`74 (78)
`35 (NP)
`57 (66)
`35 (40)
`86(87)
`
`%of
`LOH
`
`21
`27
`19
`25
`23
`26
`32
`28
`30
`19
`18
`27
`27
`12
`24
`22
`13
`
`DJ7S746. Tumor 63 was informative and unaltered at the Dl7S702,
`GAS, Dl7S846, and Dl7S856loci but was deleted for the upper allele
`of D17S776. In this patient the STS marker Dl7S746 was not infor(cid:173)
`mative. Tumor 117 was informative and unaltered at the Dl7S702,
`D17S776, and Dl7S856 loci but was deleted for the upper allele of
`Dl7S846. In this patient DJ7S746 was not informative.
`The genotypes of these four tumors and seven additional tumors for
`loci lying between Dl7S250 and D17S579 is shown in Fig. 2. Ten of
`the tumors examined in this study have clearly defined interstitial
`deletions within the BRCAJ interval, while tumor 127 appears to have
`lost a large portion of the long arm of chromosome 17. In this study
`a total of nine tumors appeared to have lost an entire chromosome 17q
`arm, since all markers in the BRCAJ region as well as telomeric
`m~~ers, such 1!5 D17S4, were ~eh:te~· ~~ ot!ter t4mors had ~OH ;lt
`all the markers in the BRCAI region but were informative and retained
`heterozygosity at D17S4. These data taken together indicate that the
`smallest commonly deleted region is located between D17S846 and
`DJ7S746. This conclusion is both consistent with and extends previ(cid:173)
`ous studies in which fewer loci were examined within the BRCA I
`region (2, 3, 16). Dl7S846 and DI7S746 are located on two overlap(cid:173)
`ping recombinant Pl bacteriophage clones. The distance between
`them is estimated to be 120-150 kilobases based on physical mapping
`data2 and could possibly contain several undiscovered genes.
`The increased availability of polymorphic STS markers in the
`region of BRCAI has also led to a continued shrinkage of the size of
`this region through genetic linkage studies in breast and breast/ovarian
`cancer families. Thus, in successive studies the telomeric border has
`moved centromerically from Dl7S579 (18, 20, 21) to DJ7S183
`(located between Dl7S750 and Dl7S579; Fig. 2) (26) to Dl7S78
`(located between Dl7S750 and DI7Sl83; Fig. 2) (33). Similarly the
`centromeric border has moved in the telomeric direction from
`Dl7S250 (19, 20, 31) to THRAJ (21, 30) to DJ7S857 (13) to DI7S702
`(34). The region we have defined as containing the target gene for
`LOH on chromosome 17q21 in sporadic breast tumors is compatible
`with these linkage studies defining BRCAI in familial breast and
`breast/ovarian cancer families. However, there is one report (29)
`which is potentially inconsistent with this conclusion. They show that
`in one family having the familial breast/ovarian cancer syndrome, one
`
`2 H. Albertsen et a/., manuscript in preparation.
`
`affected member had a recombinational event telomeric of the locu.~
`DI7S776. This locus is more telomeric than D/7S746 which is the
`telomeric boundary of the affected region defined in our study (Fig.
`2). There are at least three explanations for this apparent paradox: (a)
`the locus we have defined may be relevant only in sporadic breast
`cancer and not in hereditary breast cancer; (b) possibly there are two
`closely linked genes which are independently altered in breast-only
`versus breast/ovarian families. A comparison of the linkage studies
`done in breast-only families versus those done in breast/ovarian
`families show that in the former group the altered gene lies between
`THRAI and Dl7S579 (35), whereas in the latter group the location of
`the altered gene lies distal to Dl7S776 and proximal to Dl7S78
`(29, 32). The region we have defined is consistent with the current
`linkage analysis of the location of the altered gene in the breast-only
`families; (c) our results are not incompatible with the linkage data of
`Goldgar et al. (29). However, this would require that the BRCAJ gene
`is large (1-2 megabases) and that the recombinational event described
`by Goldgar et al. occurred within the gene. There are precedents for
`each of these requirements. For instance, the DCC gene on chromo-
`
`20
`117
`63
`26
`TL TL TL TL
`
`0175702
`
`0175746
`
`... ... ..........
`• ..- -
`-
`GAS -I
`0175846 ... -.. ... ... -...
`--
`-
`.....
`...
`... .......
`
`0175776
`
`I
`.
`""(: ~
`. ,,, .
`.... .
`0175856 -
`...
`
`"
`
`~
`
`6- ~
`
`Fig. I. Autoradiographs of four tumors for the six STS polymorphic markers between
`D/7S702 and D/75856. Arrows, deleted allele indicating LOH. Tumor 20 is deleted for
`GAS and DI7S846; tumor 26 is deleted for DI7S746, tumor 63 is deleted for Dl7Sn6;
`and tumor 117 is deleted for 0175846. T, tumor; L, lymphocyte.
`2549
`
`Downloaded from
`
`cancerres.aacrjournals.org
`
`on August 27, 2013. © 1994 American Association for Cancer
`Research.
`
`GeneDX 1032, pg. 2
`
`

`

`Case 2:13-cv-00640-RJS Document 103-11 Filed 08/31/13 Page 5 of 6
`
`BRCAI IN SPORADIC BREAST CARCINOMAS
`
`PRa!E
`
`TI.M:R
`
`Fig. 2. Genoty~ of lltumors between STS
`markers D17S250 and DJ7S579. e. markers
`with LOH {i.e., deleted); 0, STS markers whicb
`are informative and normal; e. either the tumor
`was not examined for that marker, or the marker
`was not informative. The commonly deleted
`region is indicated at the right side of the figute.
`The genetic order of the STS marker probes is
`according to published linkage studies (17, 26).
`
`11.2
`
`12
`
`21.1
`21.2
`
`21.3
`
`22
`
`23
`
`24
`
`25
`
`17Q
`
`0175250
`n ttA1
`
`0175857
`
`0175702
`GAS
`
`0175746
`
`0175776
`
`0175856
`
`0175855
`
`017S902
`
`0175579
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0 Informative and retention of heterzygosity
`
`44
`
`62
`
`89
`
`130
`
`20
`
`26
`
`63
`
`16
`0
`
`117 30
`0
`
`127
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0
`
`0 0
`
`0
`
`0
`
`0
`
`0 • • 0
`0 • • 0
`0 • • • • • • • • • 0
`0175700 • • 0 • 0
`0 • 0 • 0
`0 • 0
`0 • 0
`0 •
`0 • 0
`0 0 •
`0 0 • • • • • 0 • • •
`0175846 • • • • • • 0
`0 • • • I~
`0 • • 0 • 0 • • • • •
`0 • 0
`0 • • • 0 • •
`0 • 0 • 0
`0 •
`0 • • • • • 0 • •
`0175648 • 0
`0 • 0 • • 0 • • • • •
`0 • • 0
`0 • 0 •
`017S859 • • 0 • • • • • • • •
`0175750 • 0
`0 • 0 • • •
`0175183 • • • • • 0
`0 • 0 • •
`0 •
`0 • 0
`• Deleted
`• Not informative or not done
`
`some 18q is approximately 1.4 megabase5 (36), and the Duchenne
`muscular dystrophy (DMD) gene on Xp21 is approximately 2.3
`megabases (37). In the search for the DMD gene, linkage analysis was
`somewhat confusing because of the frequency of recombination
`events within such a large gene (38-40). aearly, identification of the
`target gene(s) in sporadic breast carcinomas as well as the familial
`breast and breast/ovarian carcinoma loci will be required to distin(cid:173)
`guish between these possibilities.
`
`References
`
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`regioos on chromosome 17q in primary human breast carcinomas wbicb are fre(cid:173)
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`
`on August 27, 2013. © 1994 American Association for Cancer
`Research.
`
`GeneDX 1032, pg. 3
`
`

`

`Case 2:13-cv-00640-RJS Document 103-11 Filed 08/31/13 Page 6 of 6
`BRCAI IN SPORAOIC BREAST CARCINOMAS
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`2551
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`GeneDX 1032, pg. 4
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`

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