Chapter 20 / Inversion Chromosomes 289 20 Inversion Chromosomes Orsetta Zuffardi, PhD, Roberto Ciccone, PhD, Sabrina Giglio, MD, PhD, and Tiziano Pramparo, PhD CONTENTS INTRODUCTION CLASSICAL CHROMOSOME INVERSIONS: EPIDEMIOLOGICAL DATA RECOMBINANT CHROMOSOMES FROM CARRIERS OF CLASSICAL HETEROZYGOUS INVERSIONS CRYPTIC INVERSIONS ASSOCIATED WITH SEGMENTAL DUPLICATIONS CRYPTIC INVERSION AT 8P23 CARRIERS OF THE 8P23 INVERSION: ARE THEY AT RISK FOR UNBALANCED OFFSPRING? OTHER CHROMOSOME REARRANGEMENTS MEDIATED BY CRYPTIC PARACENTRIC INVERSION CONCLUSIONS AND PROSPECTIVES REFERENCES INTRODUCTION A number of findings revealed that chromosome inversions are more frequent than deduced from classical cytogenetic studies. Indeed, some paracentric cryptic inversions have been found to be flanked by segmental duplications, either causing a Mendelian disease owing to the interruption of specific genes at inversion breakpoints or being present in the normal population as a polymorphism. In the latter case, in the heterozygous state they predispose to further unbalanced rearrangements such as inv dup rearrangements or simple deletions and duplications. The importance of this susceptibility factor has been well clarified with respect to some genomic disorders involving chromosome 8p and it is now emerging as a possible model that may explain the genetic basis of other recurrent chromosome rearrangements. CLASSICAL CHROMOSOME INVERSIONS: EPIDEMIOLOGICAL DATA Chromosome inversions are the most common rearrangement differentiating humans and the great ape species at the karyotypic level (1–4). Inversions in which a breakpoint is in heterochromatic regions (1qh, 9qh, 16qh, and Yq) are relatively frequent and are regarded as variants. The most common inversion not involving centromeric heterochromatin is the From: Genomic Disorders: The Genomic Basis of Disease Edited by: J. R. Lupski and P. Stankiewicz © Humana Press, Totowa, NJ 289 290 Part IV / Genomic Rearrangements and Disease Traits inv(2)(p11q13) that is also considered a benign variant. Other polymorphic inversions are also frequent and include inv(5)(p13q13) and inv(10)(p11q21.2) (5). Apart from these cases, inver- sions are approx 10 times more rare than the other balanced rearrangements (Robertsonian translocations: 1 in 1000; reciprocal translocations: 1 in 625; [6]) having a frequency ranging from approx 0.012 to 0.07% for the pericentric inversions and approx 0.01 to 0.05% for the paracentric inversions (7). In contrast to translocations for which the most frequent cause of ascertainment is the presence of reproductive difficulties, the majority of inversions are ascer- tained at prenatal diagnosis or because of an abnormal phenotype (5). The risk of unbalanced offspring from an inversion carrier, putting together the data of pericentric and the paracentric inversions, is approx 1%, much lower than that of reciprocal translocation carriers (2.7% in families ascertained through a balanced proband and 19.2% among the families ascertained through an unbalanced proband) (5). Accordingly, the reproductive fitness of inversion carri- ers is 0.926 ± 0.085, higher than that of reciprocal translocation carriers (0.70 ± 0.048; [8]). Reproductive fitness in Robertsonian translocation carriers varies between 0.768 ± 0.056 for the D/D carriers and 0.921 ± 0.123 for the D/G carriers (8). RECOMBINANT CHROMOSOMES FROM CARRIERS OF CLASSICAL HETEROZYGOUS INVERSIONS Studies on inversion heterozygotes in man and in other species have reported crossover suppression in the inverted region (9) and increased recombination elsewhere on the same chromosome (10). When recombination occurs within the inverted region between the normal and the inverted chromosomes two complementary recombinant chromosomes arise. Each of them is duplicated for the distal region of one arm and deleted for the opposite one. In the case of paracentric inversions the two recombinants are dicentric and acentric. The size of the inversion seems to be the main factor influencing the type of synapsis between the inverted and the normal chromosome. For a more complete discussion on this topic, see ref. 7. CRYPTIC INVERSIONS ASSOCIATED WITH SEGMENTAL DUPLICATIONS In the last 15 years, a series of submicroscopic paracentric inversions have been discovered while studying specific genes at a genomic level. Some of these inversions lead to the breakage of a dosage sensitive gene and, therefore, cause a Mendelian disease, other inversions break within either an extragenic region or disrupt nondosage sensitive genes and are, thus, consid- ered benign. Most of these cryptic inversions are mediated by large (usually >10 kb), highly homologous low-copy repeat (LCR) structures (also called segmental duplications or duplicons) that can act as recombination substrates in nonallelic homologous recombination (NAHR). There are clear evidences that some of the benign inversions are not mere neutral polymorphisms but may predispose to other rearrangements. The story began in 1993 when Lakich et al. (11) discovered that nearly half of the patients with severe haemophilia A had a breakage of the factor VIII gene caused by an inversion mediated essentially by intrachromatid recombination between DNA sequences in the A gene in intron 22 and one or other of two inverted copies of this sequence (int22h-2, int22h-3) located, respectively, 500 and 600 kb more telomeric. A few years later a similar mechanism was shown to be responsible for 13% of Hunter disease patients. In this case the inversion occurs because of abnormal recombination between the IDS gene and its pseudogene located 90 kb away, resulting in the disruption of the Chapter 20 / Inversion Chromosomes 291 gene (12). Other recurrent cryptic inversions mediated by homologous LCRs have been reported in normal individuals and, at least some of them, are regarded as benign. The inversion at the Xq28 emerin/filamin region was found while trying to elucidate the discrepancies observed between the genetic and physical map distances (13). This inversion, present in the heterozygous state in 33% of females and in the hemizygous state in 19% of males, is mediated by two 99% sequence identical segmental duplications flanking the emerin and filamin genes. Although inversion carriers are completely normal, some of the emerin deletions associated with Emery-Dreifuss muscular dystrophy have been hypothesized to be the result of inversion- mediated rearrangements (14). Moreover, it is not impossible that some of the dicentric X chromosomes pter-qter::qter-pter (15) are formed as a consequence of unequal crossovers between the same LCRs that mediate the inversions. Another recurrent benign cryptic inversion has been detected at the region surrounding the NPHP1 locus at 2q13. Saunier et al. (16) discovered that homozygous deletion of 290 kb responsible for nephronophthisis 1 is mediated by two copies of segmental duplications with the same orientation. These LCRs are surrounded and partially embedded into two homolo- gous segmental duplications having opposite orientation and mediating an approx 500-kb inversion present in 1.3% of the population in the homozygous state. No negative effect has been demonstrated in association with this inversion. It is obvious that embryos with any dicentric chromosome 2pter-2q13::2q13-2pter would not be viable. The paradigmatic situation is that of the Y chromosome. This chromosome has an abun- dance of LCR (amplicons), which render this chromosome susceptible to a multitude of rear- rangements that, when involving the long arm, are often the cause of spermatogenic failure (see Chapter 19) (17). It has been assumed that the polymorphisms observed at loci on the Y chromosome and mtDNA are selectively neutral and, therefore, existing patterns of molecular variation could be used to deduce the histories of populations in terms of drift, population movements, and cultural practices. However, Jobling et al. (18) demonstrated that the 3-Mb Yp inversion present in the male population is the preferential background for the PRKX/PRKY translocation underlying most XX males and some XY females (Fig. 1). This is a clear dem- onstration that this Y inversion “polymorphism” is not neutral. It seems likely that other cryptic inversions are responsible for the complex series of deletions and duplications mediated by several types of LCRs associated with the AZFc locus (19,20). CRYPTIC INVERSION AT 8p23 The finding that a Y chromosome inversion was the basis for a recurrent translocation (18) was at first considered peculiar to the sex chromosomes. Further relevance of these data emerged following our studies (21) reporting that some recurrent chromosome rearrangements at 8p occur as a consequence of an 8p submicroscopic paracentric inversion present in the parent transmitting the abnormal chromosome. At that time, we already knew that the recurrent inv dup(8p) rearrangement, an inverted duplication of the chromosome 8 short arm associated with deletion of the very distal 8p (8p23.2-pter), was not the primary product of an abnormal recombination but instead was produced by the breakage of a dicentric chromosome 8qter- 8p23.1::8p23.1-8qter (22) leading to the formation of an inv dup(8p) and, though formally not demonstrated, to a chromosome 8 deleted for part of its short arm (8p-) (Fig. 2). In the dicentric chromosome the two duplicated regions are separated by a small single copy region (Fig. 3). The fact that the original inv dup (8p) was a dicentric chromosome led us to hypothesize that 292 Part