A 122.5-kilobase deletion of the P gene underlies the high prevalence of oculocutaneous albinism type 2 in the Navajo population

Abstract

Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder. There are four known types of OCA: OCA1-OCA4. The clinical manifestations of all types of OCA include skin and hair hypopigmentation and visual impairment. Although there are a few documented observations of high frequency of albinism among Native Americans, including the Hopi, Zuni, Kuna, Jemez, Laguna, San Juan, and Navajo, no causative molecular defect has been previously reported. In the present study, we show that albinism in one Native American population, the Navajo, is caused by a LINE-mediated 122.5-kilobase deletion of the P gene, thus demonstrating that albinism in this population is OCA2. This deletion appears to be Navajo specific, because this allele was not detected in 34 other individuals with albinism who listed other Native American origins, nor has it been reported in any other ethnic group. The molecular characterization of this deletion allele allowed us to design a three-primer polymerase chain reaction system to estimate the carrier frequency in the Navajo population by screening 134 unrelated normally pigmented Navajos. The carrier frequency was found to be approximately 4.5%. The estimated prevalence of OCA2 in Navajos is between approximately 1 per 1,500 and 1 per 2,000. We further estimate that this mutation originated 400-1,000 years ago from a single founder.

Figure 1

Southern blot analysis of BamHI, XbaI, and BglI digests of genomic DNA from both a Navajo individual with OCA2 (N5) and a control subject (C). A, The hybridization was performed with a cDNA probe corresponding to exons 8–11 of the P gene. The arrows show the fragments missing in N5. B, The cDNA probe corresponds to exons 11–15 of the P gene. Note that no hybridizing fragments are detected in N5. C, The cDNA probe corresponds to exons 15–20 of the P gene. Note that no hybridizing fragments are detected in N5. Sizes of the hybridization fragments (calculated from molecular standards) are shown to the left of each panel.

Figure 2

A, Breakpoint-spanning fragment amplified by primers MHB1359 and MHB1334. In a Navajo individual with OCA2 (N5), a 1.2-kb fragment amplified, whereas in the control subject (C), no fragment was detected. B, Sequences flanking the breakpoints. The breakpoints are represented as vertical dashed lines, which are located at positions intron 9 + 13636 bp and intron 20 −6592 bp. As shown above, 122.5 kb of the P gene is deleted, including exons 10–20. The primers, MHB1359/1334, were used to amplify across the breakpoints (panel A) and the three primers, MHB1370/1333/1334, were used for detecting carriers. Microsatellite markers MHB001, MHB002, MHB003, and the SNP were used in haplotype analysis. MHB001, located 8.6 kb upstream of the left-hand breakpoint, consists of a perfect (CA)₂₃ repeat (corresponding to the 466-bp allele). The SNP (T/C) is 703 bp upstream of the left-hand breakpoint. MHB003 is 118 bp upstream of the left-hand breakpoint and consists of compound repeat (CA)₁₀(TA)₁(CA)₄. MHB002 is 20 kb downstream of the deletion and consists of a perfect (CA)₁₇ repeat (corresponding to the 370-bp allele). At the breakpoint juncture, two LINE sequences (thin arrows) are at each end and are oriented in opposite directions. The two homologous LINE sequences (white arrows) are 3,032 bp downstream of the left-hand breakpoint and 1,481 bp upstream of right-hand breakpoint. The homologous LINE sequences share 85% identity in a 745-bp stretch and are oriented in the same direction. C, Chromatograph of the sequence flanking the breakpoints.

Figure 3

PCR analysis of the deletion in affected individuals (N4 and N5), parents of N4 (N2 and N3, who are obligate carriers), and a control subject (C). Primers are shown in fig. 2B. In the control subject, amplification with primers MHB1333/1334 results in a 257-bp fragment, whereas, in carriers, primers MHB1370/1334 gave an additional 606-bp fragment. In Navajos with OCA2, only the 606-bp fragment is amplified. M = molecular ladder.