Sequence improvements and increased variant representation in the human genome reference
assembly are priorities for the GRC. This blog post describes two updates in the recent
GRCh38.p7 patch release affecting
the DUX4 region located at the chromosome 4q sub-telomere: (1) a FIX patch correcting the chromosomal representation (KQ983257.1)
and (2) a NOVEL patch
representing a variant of the region (KQ983258.1)
. A third haplotype of DUX4 region which is represented in GRCh37 will be also described.
The DUX4 region contains tandem arrays of a 3.3
Kb D4Z4 macrosatellite repeat located in the sub-telomeric region of chromosome 4q. The number of D4Z4 repeats is highly polymorphic, ranging from 8 to 100 copies in the healthy individuals,
but only 1 to 10 units in individuals with Facioscapulohumeral muscular
dystrophy-1 (FSHD1:
MIM#158900). The contraction of the repeat arrays is believed
to result in a decreased epigenetic repression effect of D4Z4 and subsequent
transcriptional activation of the DUX4 gene. Three main haplotypes, known as 4qA, 4qB and
4qA-L, have been reported for this region (1-3). The 4qB haplotype has homology to 4qA in the D4Z4 repeats, but is completely different in the distal region (1,2). 4qA, considered the reference haplotype, is the ancestral and most common haplotype. 4qA and 4qA-L are associated with FSHD, while 4qB is not (2). The different haplotypes exhibit population stratification (3).
The GRC received user feedback that the DUX4 region is incorrectly represented on chromosome 4 of the GRCh38 assembly. The repeat structure in the region complicates both sequencing and assembly. Clones representing both the 4qA and 4qB haplotypes are present in GRCh38, creating a haplotype expansion and accompanying "false" gap at NC_000004.12: 190,123,122 bp, between components AC225782.3 (WI2-3035O22; 4qB) and AC215524.3 (ABC7-42391500H16; 4qA (partial)) (Figure 1, top). In the GRCh38.p7 fix patch scaffold KQ983257.1, the GRC provides a complete representation for the 4qA haplotype by replacing AC225782.3 with
CT476828.7 (RP11-242C23) and eliminating the gap (Figure 1, bottom). The patch provides 14 copies of the DUX4 repeat. This fix patch representation for the region will be incorporated into chromosome 4 in the as yet unscheduled GRCh39 assembly release, and the 4qB representation currently present on the GRCh38 chromosome will be provided as an alternate loci scaffold.
 |
| Figure 1 Top: DUX4 region in
GRCh38. Incomplete representation of DUX4 gene in GRCh38 due to a mix
haplotype representation of 4qB and partial 4qA. Bottom: DUX4 fix
patch in GRCh38.p7. The gap is closed and a complete representation of
the 4qA haplotype is provided.
|
The GRCh38.p7 release also includes KQ983258.1 as novel patch scaffold providing representation for the variant
4qA-L haplotype. This variant is very
similar to haplotype 4qA (Figure 2, top, green dashed line) but diverge in the distal-most DUX4 copy (Figure 2, top, red dashed line) which is about 1.6 Kb larger in 4qA-L (Figure 2, bottom). The functional implication of this difference is not yet known.
 |
| Figure
2 Top: Novel patch representing
DUX4 variant 4qA-L. This variant is similar to haplotype 4qA but the
region distal to last D4Z4 unit is longer in 4qA-L. Bottom: Schematic of
D4Z4 repeat arrays for 4qA and 4qA-L regions, adapted from Lemmers et al., 2010. |
References:
1. van
Geel, M. et al. Genomics 79, 210–217 (2002)
2. Lemmers,
RJLF. et al. Nature Genetics 32, 235-236 (2002).
3. Lemmers,
RJLF. et al. Science 329, 1650-1653 (2010).
