1. Recombination between Palindromes P5 and P1 on the Human Y Chromosome Causes Massive Deletions and Spermatogenic Failure 
Sjoerd Repping, Helen Skaletsky, Julian Lange, Sherman Silber, Fulco van der Veen, Robert D. Oates, David C. Page, Steve Rozen 
The American Journal of Human Genetics 
Volume 71, Issue 4, Pages (October 2002)
DOI: /342928
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

2. Figure 1
Deletions between P5 and P1 and between P4 and P1 in relation to the sequence of the Y chromosome. A, Triangular dot plot, encompassing P5, P4, and AZFc (which contains P1, P2, and part of P3). The baseline represents 8 Mb of Y-chromosome long-arm sequence. This triangular display avoids the redundant, artifactual symmetries that would appear in a square self-versus-self plot. Each dot within the plot represents 100 bp of identity between two parts of the Y chromosome in a window of 100 bp. Direct repeats appear as horizontal lines of dots, and inverted repeats appear as vertical lines. Palindromes appear as vertical lines that almost intersect the baseline. Five major palindromes are labeled “P1” through “P5” from right to left, and arrows along the baseline indicate the extents of their inverted-repeat arms. P1.1 and P1.2 are minipalindromes within P1 (see also fig. 6). The arms of P1.1 and P1.2 are too short (10 kb) to be visible at this scale. The “b2” and “b4” direct repeats that bound AZFc are shaded blue on the baseline. Sequences that are homologous between P5 and P1 are shaded orange and green on the baseline. Diagonal gray guide lines connect the P5-P1 homologous sequences on the baseline to the two areas within the plot that contain the corresponding dots. These areas are shaded orange and boxed. The prominent triangle of dots near the baseline and labeled “DYZ19” is a satellite repeat array. B, STSs used for low-resolution breakpoint mapping. Tick marks show STS positions; asterisks indicate new STSs. STSs used in the original definition of AZFb are in boldface. Results for sY1227 and sY1228 are difficult to represent at this scale; see table A1. C, Low-resolution plus/minus STS results and deletion breakpoint positions for 12 men with spermatogenic failure. At the left are the identifiers of the men studied, and to the right of each man’s identifier is a representation of those parts of his Y chromosome that were determined to be present or absent. Horizontal black bars indicate confirmed presence of Y-chromosome DNA, and minuses indicate confirmed absence of Y-chromosome DNA, as assayed by low-resolution STSs. White boxes represent STS positives that were disregarded because of cross-amplifying loci elsewhere and because of negative results for flanking STSs. Horizontal gray bars represent the intervals to which breakpoints were localized by low-resolution breakpoint mapping. (Where STSs fall within gray bars, their results were positive). Short red vertical lines indicate the locations of amplified breakpoint junctions for nine of the patients and, for AMC0111, the 10-kb interval to which high-resolution STS mapping localized the distal breakpoint. AZFc-deleted patient WHT3060 is shown for comparison. D, Genes with significant confirmed or predicted ORFs (see the “Electronic-Database Information” section). E, Spliced but apparently noncoding transcripts (see the “Electronic-Database Information” section).
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

3. Figure 2
FISH, showing DAZ clusters in an unaffected man and in a man with a P5/proximal-P1 (AZFb) deletion. A, Representative interphase nucleus from a fertile, male control individual hybridized with cosmid 18E8 (yellow), showing two dots (corresponding to two DAZ clusters, each containing two DAZ genes). B, Representative interphase nucleus from P5/proximal-P1–deleted patient WHT4396, showing one dot (corresponding to one DAZ cluster). C, Histogram of number of nuclei observed grouped by number of dots per nucleus.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

4. Figure 3
P5/P1 deletion junctions, indicating homologous recombination as the cause of the deletion. A, Junction sequence in AMC0110 aligned with proximal and distal Y-chromosome reference sequence. Dots indicate base pairs identical to the junction sequence. B, Model of production of the deletion-junction sequence in AMC0110 by homologous recombination. The bases shown (C/T, A/G, and C/T) differ between the proximal and distal copies of the sequence and therefore define the location of the deletion breakpoint within the junction sequence. C, Junction sequence in WHT4396 aligned with proximal and distal Y-chromosome reference sequence. D, Junction sequence in WHT2943 aligned with proximal and distal Y-chromosome reference sequence. E, Junction sequence in WHT3516, WHT3642, WHT4426, and WHT4486 aligned with proximal and distal Y-chromosome reference sequence.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

5. Figure 4
P5/distal-P1 deletion junction in WHT3410. A, Junction sequence aligned with proximal and distal Y-chromosome reference sequences. Ovals mark 3 bp that differ between WHT3410 and the Y-chromosome reference sequence. The white box marks the 3 bp that contain the deletion junction. B, Breakpoint locations within palindrome P5 and minipalindrome P1.1, and the resulting sequence organization in WHT3410. Orange and green shading is as in figures 1 and 6.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

6. Figure 5
P4/distal-P1 deletion junction in WHT2825. Junction sequence is aligned with proximal and distal Y-chromosome reference sequence.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

7. Figure 6
“High-magnification” dot plots of the two regions of high similarity between P5 and P1 (see fig. 1A). Each dot represents 50 bp of identity in a window of 50 bp. Orientation and orange and green shading is as in figure 1A. A, Central P5 versus P1.2 and the neighboring region of the proximal arm of P1. Locations of the P5/proximal-P1 deletions in AMC0110 and WHT4396 are indicated by red arrows. (The coordinate of a deletion in the plot is the location of the proximal breakpoint paired with the location of the distal breakpoint. Deletions that extend between direct repeats map to horizontal lines of dots.) B, Central P5 versus P1.1 and the neighboring region of the distal arm of P1. Locations of the P5/distal-P1 deletions in WHT2943, WHT3410, WHT3642, WHT3516, WHT4426, and WHT4486 are indicated. WHT3410’s deletion does not extend between homologous sequences and therefore does not map to a line of dots.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions

8. Figure 7
Previous model of recurrent, interstitial Y-chromosome deletions that cause infertility in men (Vogt et al. 1996) contrasted with current model.
The American Journal of Human Genetics  , DOI: ( /342928)
Copyright © 2002 The American Society of Human Genetics Terms and Conditions