HUMAN MUTATION 27(2),133^137,2006

RAPID COMMUNICATION

Paternal Uniparental Isodisomy of the EntireChromosome 3 Revealed in a Person With NoApparent Phenotypic Disorders

Peng Xiao,1,2 Pengyuan Liu,1,2 James L. Weber,3 Christopher J. Papasian,4 Robert R. Recker,1,2

and Hong-Wen Deng4–8�

1Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, Nebraska; 2Osteoporosis Research Center, School ofMedicine, Creighton University, Omaha, Nebraska; 3Center for Medical Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin;4Department of Basic Medical Science, School of Medicine, University of Missouri–Kansas City, Kansas City, Missouri; 5Department ofOrthopedic Surgery, School of Medicine, University of Missouri–Kansas City, Kansas City, Missouri; 6Key Laboratory of Biomedical InformationEngineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Shanxi, P. R. China; 7Institute ofMolecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Shanxi, P. R. China; 8Laboratory of Molecular andStatistical Genetics, College of Life Sciences, Hunan Normal University, Hunan, P. R. China

Communicated by Haig H. Kazazian, Jr.

Uniparental disomy (UPD) is a rare genetic abnormality. During a whole genome linkage study we identified acase of paternal uniparental isodisomy 3 serendipitously. This is the first ascertained human paternal UPD forchromosome 3 (UPD3pat). The finding of this paternal UPD case of the entire chromosome 3 with no apparentphenotypic disorders suggests that there are no paternal imprinted genes causing rare genetic disorders onchromosome 3. Hum Mutat 27(2), 133–137, 2006. rr 2006 Wiley-Liss, Inc.

KEY WORDS: uniparental disomy; UPD; UPD3; isodisomy; paternal; imprinted

INTRODUCTION

The concept of uniparental disomy (UPD) was introduced in1980 to describe a condition in which an individual inherits twocopies of a chromosome pair from one parent and no copy from thesecond parent [Engel, 1980]. UPD may be classified as eithermaternal or paternal depending on the parental origin of thedisomic chromosome. Further classification of UPD depends onwhether the two inherited chromosomes represent duplicatecopies of a single parental chromosome (isodisomy) or the twoinherited chromosomes represent both chromosomes in the pairfrom the sole parental donor, without duplication (heterodisomy).As a rare abnormality, UPD may result in rare recessive disordersor developmental aberrances due to imprinting effects, and mayalso occur with no apparent phenotypic effects [Ledbetter andEngel, 1995]. The first case of UPD in humans was recognized onchromosome 7 of a child with cystic fibrosis and short stature[Spence et al., 1988]. This discovery led to exploration of theassociation of UPDs occurring on other chromosomes in variousinheritable diseases. Genetic imprinting and autosomal recessive-ness are two prominent mechanisms for diseases resulting fromUPD [Engel, 1980, 1998]. The first human case of UPD with animprinting effect was identified in a patient with Prader-Willisyndrome [Purvis-Smith et al., 1992]. Other imprinting effects ofUPD have been associated with different human chromosomes(for review see Ledbetter and Engel [1995]). Similarly, since theinitial discovery of cystic fibrosis as the first human UPD case of anautosomal-recessive disease [Spence et al., 1988], an autosomal-

recessive mechanism has been implicated in several additionalhuman diseases attributable to UPD [Cervantes et al., 2002;Hannula et al., 2002; Spiekerkoetter et al., 2002]. Previous studiesdesigned to identify UPD3 in patients with genetic diseasesassociated with imprinting effects, such as Brachmann-De Langesyndrome [Shaffer et al., 1993; De Marchi et al., 1994], failedto identify any patients with UPD3. Although two maternalUPD3 cases associated with recessive diseases were recentlyreported, imprinting effects have not been implicated inUPD3-associated disorders.

Here we report the first case of paternal UDP3, which weidentified serendipitously in the course of a whole genome linkagescan study designed to define regions containing quantitative traitloci (QTLs) underlying bone mineral density (BMD) variation.

Published online 20 January 2006 in Wiley InterScience (www.interscience.wiley.com).

DOI10.1002/humu.20302

Received 2 May 2005; accepted revised manuscript 7 December2005.

Grant sponsor: NHLBI Mammalian Genotyping Service; Grantsponsor: NIH; Grant numbers: K01 AR002170-01; R01 AR050496-01; and R01 GM060402-01A1; Grant sponsor: State of Nebraska;Grant numbers: LB595; and LB692.

�Correspondence to: Hong-Wen Deng, Ph.D., Departments ofOrthopedic Surgery and Basic Medical Science, School of Medicine,University of Missouri^Kansas City, Room M3-C03,2411Holmes St.,Kansas City, MO 64108. E-mail: dengh@umkc.edu

rr 2006 WILEY-LISS, INC.

The individual with paternal isodisomy of the entire chromosome3 had no apparent phenotypic defects.

MATERIALSANDMETHODS

In the context of a study designed to identify genomic regionsthat contain QTLs underlying BMD variation, we performed awhole genome linkage scan on 4,251 subjects from 471 pedigreesusing 410 microsatellite markers. The study was approved by theCreighton University Institutional Review Board, and bloodspecimens were collected from patients at the CreightonUniversity Medical Center. Genomic DNA was extracted fromwhole blood using a commercial isolation kit (Gentra Systems,Minneapolis, MN, www.gentra.com/products.asp) and sent to theMarshfield Center for Medical Genetics, where the genotypingwork was performed. Information for all of the markers used can befound in Screening Set 14 on the Marshfield website (http://research.marshfieldclinic.org/genetics/sets/combo.html). The initialdata analysis suggested that one person in the study had a paternalUPD of chromosome 3 (UPD3pat).

To further explore potential mechanisms for the observedUPD3pat, a cytogenetic analysis was performed on the father ofthe child with UPD3. This additional analysis was also approved bythe Creighton University Institutional Review Board. First, 5 ml ofperipheral blood were drawn into a sodium-heparin tube atambient temperature and immediately transferred to the HumanGenetics Laboratory at the University of Nebraska Medical Center(UNMC, about 1 mile away). The blood was placed in alymphocyte culture media (72EB, ethidium bromide) tube andmixed by gentle inverting, and the pH was adjusted to 7.2–7.4with 0.1 M HCl or 0.2 M NaOH. The culture was placed in a slantrack in a 371C incubator and incubated for 72 hr. Approximately35 min prior to the scheduled harvest, 200ml of Colcemid wereadded to the culture tube with a micropipette. Cultures wereharvested according to the standard operating procedure for bloodcultures established in the laboratory. Standard G-bandingprocedures were performed on the cell cultures in prometaphase/metaphase [Davisson and Akeson, 1987]. Photomicrographs weretaken for routine karyotype analysis.

RESULTS

During evaluation of the whole genome linkage scan study, weobserved interesting incompatibilities in one family between onechild (Child 1) and his mother on chromosome 3 (Fig. 1). DNAsfrom both children and both parents in the family were wellamplified, and marker-locus genotyping error was only 0.3% in thiswhole genome scan study, so these incompatibilities betweenmother and Child 1 did not appear to be attributable to technicalfactors. Further examination of the genotypes on chromosome 3for Child 1 revealed an unambiguous pattern of paternaluniparental isodisomy. Child 1 was homozygous for 25 out of 26markers genotyped on chromosome 3, and one genotype wasmissing (Fig. 1). The genotypes of 16 of the 25 homozygousmarkers in Child 1 were incompatible with the mother’s alleles,but were identical with the father’s alleles on a single homologouschromosome (Fig. 1). We could not definitively determine whethergenotypes of the other nine homozygous markers on chromosome3 of Child 1 were inherited from the father only or were ofbiparental origin, because both parents shared at least one copy ofthe same allele at each of these nine loci. However, based on the16 confirmed markers with the UPDpat pattern, it is reasonable toconclude that the homozygous alleles at the other nine marker loci

were also uniquely inherited from the father. All chromosome pairsof Child 1 (other than chromosome 3) appeared normal accordingto the genotypes of 384 markers on the other chromosomes, andChild 2 showed compatible biparental inheritance for all of themarkers genotyped on chromosome 3 (Fig. 1). These data arereadily explained by concluding that Child 1 had a paternaluniparental isodisomy for the entire chromosome 3.

The results of the cytogenetic analysis indicated a normalkaryotype (46, XY) for the father in the family (Fig. 2).

DISCUSSION

Proposed mechanisms for the development of UPD includegamete complementation, postfertilization error, trisomyrescue, and monosomic complement present in the embryo[Spence et al., 1988].

There have been only four verified cases of UPD in humansresulting from gamete complementation, and at least one of theparents in each of these cases had Robertsonian, reciprocal, or denovo translocations [Wang et al., 1991; Dawson et al., 1996; Parket al., 1998; Berend et al., 1999]. In our case the genome of thefather was normal, based on both cytogenetic (Fig. 2) andgenotypic analyses of the whole genome. Consequently, gametecomplementation would appear to be highly unlikely as amechanistic explanation for the development of UDP3.

Postfertilization errors may also account for the development ofUPD. One potential pitfall in identifying errors of somaticinheritance, however, is that analysis under conditions ofinsufficient marker density may fail to detect double crossovers.Under these conditions, a nondisjunction event may be mis-classified as a postfertilization error [Robinson et al., 2000].Double crossovers observed in several empirical studies ofCaucasians spanned 420 cM genomic regions [Kwiatkowskiet al., 1993; Weber et al., 1993; Robinson et al., 2000]. In thecurrent study the genetic distance between adjacent markersranged from 3.0 to 14.6 cM, with an average density of 8.9 cM onchromosome 3. This dense marker coverage makes it highlyunlikely that any double crossover was missed in any markerinterval, and consequently the inheritance pattern described forchromosome 3 in Child 1 does not appear to be attributable toundetected double crossovers.

Our whole genome linkage study was designed to identify QTLsunderlying BMD variation in a study of osteoporosis. For eachfamily, a proband with high or low BMD (top or bottom 10% of anage-matched population) was recruited, along with availablerelatives of the proband. During our recruitment, each visitorfilled out a detailed questionnaire and individuals with significantunderlying illness (other than illnesses associated with low BMD)were excluded as previously described [Deng et al., 2002]. Allclinical information obtained from recruited subjects was stored ina database for records. By checking these records we found that allmembers of Child 1’s family had no apparent diseases at the timeof their visit to the Osteoporosis Research Center in 2002, withthe exception of the proband (the father), who was limited to lowBMD. Child 1 was 42 years old and 175 cm tall at the time of hisvisit in 2002. The father was 26 and the mother was 19 years oldwhen Child 1 was born.

Although some genes underlying autosomal-recessive diseaseshave been identified on chromosome 3 [Minetti et al., 1998;Anikster et al., 2001; Ang et al., 2002; Fields et al., 2002], thehomozygous isodisomic Child 1, who was 42 years old when heparticipated in this study, did not display any known autosomal-recessive disease. The height of Child 1 was normal and showed no

134 HUMANMUTATION 27(2),133^137,2006

Human Mutation DOI 10.1002/humu

growth retardation. This result is, to some extent, consistent withtwo previous studies that attempted to identify UPD3 in patientswith growth retardation, but failed to identify UPD3 in any of thepatients studied [Shaffer et al., 1993; De Marchi et al., 1994]. Theauthors concluded that UPD3 was not an important cause ofgrowth retardation.

Reviews of human UPD have identified UPD of 19 humanchromosomes [Ledbetter and Engel, 1995; Kotzot, 1999, 2002];however, UPD of chromosomes 3, 12, 18, and 19 were notdescribed in those reviews. Although the existence of maternalUPD3 was proposed in 1974 [Betz et al., 1974], no cases ofmaternal UPD3 were identified until 2004. The first case ofmaternal UPD3, which was discovered on only one locus in a

patient with Fanconi-Bickel syndrome (an autosomal-recessivedisease), was reported at the 2004 American Society of HumanGenetics Meeting [Hoffman et al., 2004]. The second case was asegmental maternal UPD3 on 3q21.3-3qter for a congenitaldisorder of glycosylation type Id [Schollen et al., 2005]. Both ofthese UPD3mat-related diseases are rare recessive diseases.

To the best of our knowledge, the case we describe here is thefirst human paternal UPD identified on chromosome 3. Further-more, the current case is only the third UPD case discoveredduring a whole genome linkage scan (the other two were reportedby Field et al. [1998] and Abecasis et al. [2004]). Paternal UPDcases are encountered less frequently than maternal UPD (theratio of paternal UPD to maternal UPD is approximately 1:3

FIGURE 1. Genotypes of chromosome 3 for isodisomic Child1, normal Child 2, and the two parents.The isodisomic chromosome isshaded in black, and asterisks (�) for the mother indicate the incompatible marker genotypes between the mother and Child 1.The numbers in the second column of the ¢gure indicate the average genetic map of males and females for the listed markers (cM)obtained fromtheMarsh¢eldCenter forMedicalGeneticswebsite (http://research.marsh¢eldclinic.org/genetics/sets/combo.html).For simplicity, the alleles of each marker are denoted by 1, 2, 3, and 4 from the smallest to the largest size. Missing genotypes aredenotedbyblanks.ThechromosomeofChild 2 shadedwithgraywas inherited fromhismother. Since the speci¢cphaseof genotypesin the parents cannot be determined, it is depicted this way just for simplicity.

HUMAN MUTATION 27(2),133^137,2006 135

Human Mutation DOI 10.1002/humu

[Kotzot, 1999]), and isodisomy occurs less frequently thanheterodisomy, particularly when the entire chromosome isinvolved. Consequently, our discovery of a paternal isodisomy forthe entire chromosome 3 in the course of a whole genome scanstudy is of great interest. Moreover, if there were critical paternallyimprinted genes on chromosome 3, they would not be functionalin Child 1 due to non-expression of imprinted genes from thepaternal disomic chromosomes and lack of complementaryexpression from the maternal chromosome. This situation wouldresult in apparent phenotypic effects, such as serious geneticdiseases. However, Child 1 with UPD3pat did not display anyobvious adverse phenotypic disorders even at age 42, which atteststo the fact that all phenotypically important genes on the paternalchromosome 3 were expressed even without complementaryexpression from the maternal chromosome. Therefore, weconclude that there are no important imprinted genes causingsevere diseases on the paternal human chromosome 3, at least

before old age. This finding should have broad implications for theclinical genetics community, as well as for our knowledge abouthuman imprinting effects.

REFERENCES

Abecasis GR, Burt RA, Hall D, Bochum S, Doheny KF, Lundy SL,Torrington M, Roos JL, Gogos JA, Karayiorgou M. 2004.Genomewide scan in families with schizophrenia from thefounder population of Afrikaners reveals evidence for linkageand uniparental disomy on chromosome 1. Am J Hum Genet74:403–417.

Ang SO, Chen H, Hirota K, Gordeuk VR, Jelinek J, Guan Y, Liu E,Sergueeva AI, Miasnikova GY, Mole D, Maxwell PH, StocktonDW, Semenza GL, Prchal JT. 2002. Disruption of oxygenhomeostasis underlies congenital Chuvash polycythemia. NatGenet 32:614–621.

FIGURE 2. G-banding karyotype of the father. The cytogenetic analysis did not reveal any evidence of a detectable numericalor structural chromosomal abnormality at theG-banding level.

136 HUMANMUTATION 27(2),133^137,2006

Human Mutation DOI 10.1002/humu

Anikster Y, Huizing M, White J, Shevchenko YO, Fitzpatrick DL,Touchman JW, Compton JG, Bale SJ, Swank RT, Gahl WA, ToroJR. 2001. Mutation of a new gene causes a unique form ofHermansky-Pudlak syndrome in a genetic isolate of centralPuerto Rico. Nat Genet 28:376–380.

Berend SA, Feldman GL, McCaskill C, Czarnecki P, Van Dyke DL,Shaffer LG. 1999. Investigation of two cases of paternal disomy13 suggests timing of isochromosome formation and mechanismsleading to uniparental disomy. Am J Med Genet 82:275–281.

Betz A, Turleau C, de Grouchy J. 1974. Heterozygotic ethomozygotic pour un inversion pericentrique du 3 humain.Ann Genet 17:77–80.

Cervantes RB, Stringer JR, Shao C, Tischfield JA, Stambrook PJ.2002. Embryonic stem cells and somatic cells differ inmutation frequency and type. Proc Natl Acad Sci USA 99:3586–3590.

Davisson MT, Akeson EC. 1987. An improved method forpreparing G-banded chromosomes from mouse peripheral blood.Cytogenet Cell Genet 45:70–74.

Dawson AJ, Mears AJ, Chudley AE, Bech-Hansen T, McDermidH. 1996. Der(22)t(11;22) resulting from a paternal de novotranslocation, adjacent 1 segregation, and maternal hetero-disomy of chromosome 22. J Med Genet 33:952–956.

De Marchi N, Antonarakis SE, Jackson L. 1994. No uniparentaldisomy for chromosome 3 in Brachmann-De Lange syndrome.Am J Med Genet 49:133–135.

Deng HW, Deng H, Liu YJ, Liu YZ, Xu FH, Shen H, Conway T, LiJL, Huang QY, Davies KM, Recker RR. 2002. A genomewidelinkage scan for quantitative-trait loci for obesity phenotypes.Am J Hum Genet 70:1138–1151.

Engel E. 1980. A new genetic concept: uniparental disomy and itspotential effect, isodisomy. Am J Med Genet 6:137–143.

Engel E. 1998. Uniparental disomies in unselected populations.Am J Hum Genet 63:962–966.

Field LL, Tobias R, Robinson WP, Paisey R, Bain S. 1998. Maternaluniparental disomy of chromosome 1 with no apparentphenotypic effects. Am J Hum Genet 63:1216–1220.

Fields RR, Zhou G, Huang D, Davis JR, Moller C, Jacobson SG,Kimberling WJ, Sumegi J. 2002. Usher syndrome type III:revised genomic structure of the USH3 gene and identificationof novel mutations. Am J Hum Genet 71:607–617.

Hannula K, Lipsanen-Nyman M, Kristo P, Kaitila I, Simola KO,Lenko HL, Tapanainen P, Holmberg C, Kere J. 2002. Geneticscreening for maternal uniparental disomy of chromosome 7 inprenatal and postnatal growth retardation of unknown cause.Pediatrics 109:441–448.

Hoffman TL, Parton PG, De Leon D, Gadi I, Krantz I, Santer R,Stanley C, Wilson T. 2004. A case of Fanconi Bickel syndromecaused by uniparental disomy of chromosome 3 with hyper-insulinism and hyperammonemia. In: Proceedings of the Meet-ing of the American Society of Human Genetics. Abstractnumber 1841/F3.

Kotzot D. 1999. Abnormal phenotypes in uniparental disomy(UPD): fundamental aspects and a critical review withbibliography of UPD other than 15. Am J Med Genet 82:265–274.

Kotzot D. 2002. Review and meta-analysis of systematic searchesfor uniparental disomy (UPD) other than UPD 15. Am J MedGenet 111:366–375.

Kwiatkowski DJ, Dib C, Slaugenhaupt SA, Povey S, Gusella JF,Haines JL. 1993. An index marker map of chromosome 9provides strong evidence for positive interference. Am J HumGenet 53:1279–1288.

Ledbetter DH, Engel E. 1995. Uniparental disomy in humans:development of an imprinting map and its implications forprenatal diagnosis. Hum Mol Genet 4(Spec No):1757–1764.

Minetti C, Sotgia F, Bruno C, Scartezzini P, Broda P, Bado M,Masetti E, Mazzocco M, Egeo A, Donati MA, Volonte D,Galbiati F, Cordone G, Bricarelli FD, Lisanti MP, Zara F. 1998.Mutations in the caveolin-3 gene cause autosomal dominantlimb-girdle muscular dystrophy. Nat Genet 18:365–368.

Park JP, Moeschler JB, Hani VH, Hawk AB, Belloni DR, Noll WW,Mohandas TK. 1998. Maternal disomy and Prader-Willisyndrome consistent with gamete complementation in a caseof familial translocation (3;15) (p25;q11.2). Am J Med Genet78:134–139.

Purvis-Smith SG, Saville T, Manass S, Yip MY, Lam-Po-Tang PR,Duffy B, Johnston H, Leigh D, McDonald B. 1992. Uniparentaldisomy 15 resulting from ‘‘correction’’ of an initial trisomy 15.Am J Hum Genet 50:1348–1350.

Robinson WP, Christian SL, Kuchinka BD, Penaherrera MS, DasS, Schuffenhauer S, Malcolm S, Schinzel AA, Hassold TJ,Ledbetter DH. 2000. Somatic segregation errors predominantlycontribute to the gain or loss of a paternal chromosome leadingto uniparental disomy for chromosome 15. Clin Genet 57:349–358.

Schollen E, Grunewald S, Keldermans L, Albrecht B, Korner C,Matthijs G. 2005. CDG-Id caused by homozygosity for an ALG3mutation due to segmental maternal isodisomy UPD3(q21.3-qter). Eur J Med Genet 48:153–158.

Shaffer LG, Overhauser J, Jackson LG, Ledbetter DH. 1993.Genetic syndromes and uniparental disomy: a study of 16 casesof Brachmann-de Lange syndrome. Am J Med Genet 47:383–386.

Spence JE, Perciaccante RG, Greig GM, Willard HF, LedbetterDH, Hejtmancik JF, Pollack MS, O’Brien WE, Beaudet AL.1988. Uniparental disomy as a mechanism for human geneticdisease. Am J Hum Genet 42:217–226.

Spiekerkoetter U, Eeds A, Yue Z, Haines J, Strauss AW, SummarM. 2002. Uniparental disomy of chromosome 2 resulting inlethal trifunctional protein deficiency due to homozygous alpha-subunit mutations. Hum Mutat 20:447–451.

Wang JC, Passage MB, Yen PH, Shapiro LJ, Mohandas TK. 1991.Uniparental heterodisomy for chromosome 14 in a phenotypi-cally abnormal familial balanced 13/14 Robertsonian transloca-tion carrier. Am J Hum Genet 48:1069–1074.

Weber JL, Wang Z, Hansen K, Stephenson M, Kappel C, SalzmanS, Wilkie PJ, Keats B, Dracopoli NC, Brandriff BF. 1993.Evidence for human meiotic recombination interference ob-tained through construction of a short tandem repeat-poly-morphism linkage map of chromosome 19. Am J Hum Genet 53:1079–1095.

HUMANMUTATION 27(2),133^137,2006 137

Human Mutation DOI 10.1002/humu