Three novel polymorphic microsatellite markers for the glaucoma locus GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12.

Abstract

In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at 2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide (GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite markers.

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Three novel polymorphic microsatellite markers for the glaucoma locus
GLC1B by datamining tetranucleotide repeats on chromosome 2p12-q12
Carlos Murga-Zamalloa, Maria Luisa Guevara-Fujita, Alejandro Estrada-Cuzcano and Ricardo Fujita
Centro de Genética y Biología Molecular, Facultad de Medicina, Universidad de San Martín de Porres,
Lima, Perú.
Abstract
In order to identify new markers around the glaucoma locus GLC1B as a tool to refine its critical region at
2p11.2-2q11.2, we searched the critical region sequence obtained from the UCSC database for tetranucleotide
(GATA)n and (GTCT)n repeats of at least 10 units in length. Three out of four potential microsatellite loci were found
to be polymorphic, heterozygosity ranging from 64.56% to 79.59%. The identified markers are useful not only for
GLC1B locus but also for the study of other disease loci at 2p11.2-2q11.2, a region with scarcity of microsatellite
markers.
Key words: GLC1B, microsatellite polymorphic markers, tetranucleotide tandem repeat, gene mapping, glaucoma.
Received: November 12, 2008; Accepted: June 23, 2009.
Primary open angle glaucoma (POAG), an optic neu-
ropathy, is one of the leading causes of blindness (preva-
lence 3-7% worldwide), although early detection makes it
preventable (Wolfs et al., 2000). POAG heritability is high
and family studies revealed at least eight loci with only two
causative genes identified so far (Challa, 2004). Locus
GLC1B was mapped by linkage analysis in British families
to a region of about 21 Mb flanked by markers D2S176 and
D2S2161 on chromosome 2cen-q13 (Stoilova et al, 1996).
We reported a Peruvian family with POAG linked to the
GLC1B region, with an unaffected member presenting the
same haplotype as affected relatives, regarding markers
D2S2264, D2S1897and D2S176, but not sharing the alleles
atD2S417andD2S2161(Fujitaetal.,2002Guevara-Fujita
et al., 2003). The segment delimited by D2S176 and
D2S2264 was discarded for GLC1B, thus narrowing down
the locus critical region to about 15,5 Mb (Fig 1).
In order to refine the location of GLC1B, we sought
markers between D2S2264 and D2S417 which were about
15 Mb apart. However, the reported microsatellite markers
did not evenly cover this region, neither were informative
in the family we were studying.
This prompted us to search for tetranucleotide repeat
markers in the GLC1B region, since it is well recognized
that tetranucleotide motifs present better allele separation
and extra bands than dinucleotide. We searched the NCBI
HUMANGENOMEDATASEforthesemotifsmappingat
the segment of about 16 Mb between markers D2S417 and
D2S2264 at 2p11.2-2q11.2. Primers flanking candidate
markers were designed and their heterozygosity tested in
healthy non-related individuals and in our previously re-
ported POAG family. (Fujita 2002, Guevara-Fujita et al,
2003). DNA was obtained from peripheral blood of a total
of 106 healthy non-related volunteers using routine salt-
ing-out method.
Sequencesfrom2p11.2and2q11.2(betweenD2S417
and D2S2264) from NCBI BUILD 36.1 available from
‘The Human Genome Browser at UCSC’ Genomic Library
were searched for tetranucleotide repeats with (GATA)n
motifs at least 10 units long their flanking sequences, using
BIOEDIT SEQUENCE ALIGNMENT EDITOR®soft-
ware. Selected sequences were analyzed using VECTOR
NTI 8®(Demo version) for primer design calculations. Re-
actions were performed in a volume of 10 ?L, containing
50 ng of DNA, 2.5 mM each of dNTPs, 1 mM of each
primer, 1 unit of Taq polymerase and 1 ?L of 10X buffer
with 1 ?L of 10X MgCl2. PCR products were amplified on
an Amplitron II Thermolyne thermocycler cycling condi-
tions: 35 cycles of 94 °C for 30 s, optimal annealing tem-
perature for 30 s and 72 °C for 30 s. PCR products were
electrophoresed on 5 or 6% denaturing acrylamide gels, al-
leles subsequently revealed by silver staining. Allele sizes
were determined by comparison with a pUC18 sequencing
reaction product.
Genetics and Molecular Biology, 32, 4, 720-722 (2009)
Copyright © 2009, Sociedade Brasileira de Genética. Printed in Brazil
www.sbg.org.br
Send Correspondence to Ricardo Fujita. Centro de Genética y
Biología Molecular, Facultad de Medicina, Universidad de San
Martín de Porres, Alameda del Corregidor 1535, La Molina, Lima,
Peru. E-mail: rfujita@rcp.net.pe.
Present addresses: CM-Z, W.K: Kellogg Eye Center, University of
Michigan School of Medicine, MI USA; AE-C: Department of Hu-
man Genetics, Radboud University Nijmegen Medical Centre, The
Netherlands.
Short Communication

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Four sequences with a (GATA)n motif were identi-
fied on the 15,5 Mb segment between 2p11.2 and 2q11.2.
To assess heterozygosity, 106 individuals (212 chromo-
somes) were genotyped from a sample of Lima population,
a heterogeneous admixture of South American native and
Caucasian ancestries, with minor Asian and African contri-
butions. Three of the identified loci turned out to be poly-
morphic (Table 1). Figure 1 shows the relative location of
the new markersD2SCATTO3,
D2SCATTO2 and D2SCATTO1 and of the reference
markersbetweenD2S216andD2S176ontheGLC1Blocus
region on chromosome 2. Table 1 also shows the optimal
annealing temperature, allele frequencies, allele size and
heterozygosity calculated for each new marker. Marker
D2SCATTO1 showed eight alleles ranging from 244 to 272
base pairs (bp) with heterozygosity of 75.15%, marker
D2SCATTO2 eight alleles ranging from 319 to 347 bp with
heterozygosity of 79.59%, and marker D2SCATTO3 three
alleles ranging from 221 to 229 bp with heterozygosity of
64.56%.AtD2SCATTO4onlyone291bpproductwasob-
tained in the sample analyzed. Allele sizes of three of the
new polymorphic markers allow for multi-loading, making
genotyping easier and reducing lab work and time. Primer
D2SCATTO4,
Murga-Zamalloa et al.
721
Table 1 - Markers identifed in the present study, genomic location, allele sizes and frequencies, and primer sequences
Markers
Cytogenetic location
Primers
Annealing
temperature
Alleles (bp)
Frequency
Forward
Reverse
D2SCATTO3
2p11.2 (Chr2: 89399095-89399314 Mb)
GGTCCAATTCCCTGGAACCACCAG
GCCAGATAGCCAGTGGCAGGACC
62 °C
221
0.25
225
0.45
229
0.30
D2SCATTO4
2q11.2 (Chr2: 97104768-97105061 Mb)
GCACCAGGCTCTATCCTGCACC
GGGTTTCAGCTGTTTGTAACAGCC
60 °C
264
1.00
D2SCATTO2
2q11.2 (Chr2: 99437128-99437461 Mb)
TGTACTCCCTCTCCGGGGATC
GGGCCATACTGTGTTTACAGGAGC
60 °C
347
0.01
343
0.02
339
0.10
335
0.19
331
0.19
327
0.32
323
0.12
319
0.04
DS2CATTO1
2q11.2 (Chr2: 100654172-1006544369 Mb)
ACAAAACTTAGCCGGGCATGG
CAATGAACCATCACAGTCAGGG
62 °C
272
0.04
268
0.27
264
0.39
260
0.11
256
0.06
252
0.02
248
0.03
244
0.09
Figure 1 - Cytogenetic localization of 2p11.2-q11.2 markers for Primary
Open Angle Glaucoma locus GLC1B [Stoilova et al. (1996) and Fujita et
al. (2002)]. The known markers in the region flanked by D2S2161 and
D2S176 (D2S417, D2S2264, D2S1897) and generated in this work
D2SCATTO3, D2SCATTO4, D2SCATTO2 and D2SCATTO1) are
shown. . The ruler the partial map of chromosome 2 shows the relative nu-
cleotidepositionexpressedinMegabases(80Mb-110Mb,TheUniversity
of California at Santa Cruz Genome Browser Gateway).

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sequences, cytogenetic localization and allele sizes of each
marker are deposited in the NCBI dbSNP (BUILD B131,
D2SCATTO1 NCBI ss: 142466905; D2SCATTO2 NCBI
ss: 142466907; D2SCATTO3 NCBI ss: 14246691;
2D2SCATTO4 NCBI ss:142466910).
These markers can be used not only for screening
families with POAG populations (Wolfs et al., 2000), but
also in other genetic studies in region 2p11.2-q11.2 where
locifordifferentdiseasesmapped.ExamplesareAmishIn-
fantile Epilepsy Syndrome (MIM: 609056), Chronic Ob-
structive Pulmonary Disease with Severe Early-Onset
(MIM: 606963), Achromatopsia 2 (MIM: 216900) and
Ahnidrotic Ectodermal Dysplasia (MIM: 224900). The
studyofotherdiseasesmappedtheoverlappingregionsuch
as Schizophrenia (MIM: 181500), Congenital Cataract
(MIM: 607304), Combined Deficiency of Vitamin K-De-
pendent Clotting Factors (MIM: 277450), Ataxia-Telan-
giectasia (MIM: 208900), Congenital Pulmonary Alveolar
Proteinosis (MIM: 178640) Nephronophthisis (MIM:
256100) could also benefit from the use of these markers.
Acknowledgments
Universidad de San Martin de Porres Funds, Lima,
Perú (Project number E20012003005), Consejo Nacional
de Ciencia y Tecnología Perú (CONCYTEC).
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alignmenteditorfor
Associate Editor: Paulo A. Otto
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722 Microsatellite markers at locus GLC1B