Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders.
To report on initial clinical indications for CES referrals and ...molecular diagnostic rates for different indications and for different test types.
Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available.
Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES.
Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 95% CI, 1.6-33.1) of trio-CES was due to the identification of de novo and compound heterozygous variants.
In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
We examined the immunoglobulin (Ig) heavy chain variable region genes (VH genes) used by leukemia cells of 1220 unrelated patients with chronic lymphocytic leukemia (CLL). We found 1188 (97%) ...expressed Ig encoded by a single Ig VH subgroup, the most common of which was VH3 (571 or 48.1%), followed by VH1 (319 or 26.8%) and VH4 (241 or 20.2%). Using allele-specific primers, we found 13.8% of all samples (n = 164) used one major VH1-69 allele, designated 51p1, 163 of which were not somatically mutated. For these cases, there was marked restriction in the structure of the Ig third complementarity determining regions (CDR3s), which were encoded by a small number of unmutated D and JH gene segments. Strikingly, 15 of the 163 cases had virtually identical CDR3s encoded by the second reading frame of D3-16 and JH3. Further analysis revealed that each of these 15 samples used the same unmutated Ig kappa light-chain gene, namely A27. These data reveal that approximately 1.3% (15/1220) of all patients had leukemia cells that expressed virtually identical Ig. This finding provides compelling evidence that the Ig expressed by CLL B cells are highly selected and not representative of the Ig expressed by naive B cells.
We analyzed the immunoglobulin (Ig) variable heavy (IGHV) and variable light chain genes used by leukemia cells of 258 unrelated patients with chronic lymphocytic leukemia (CLL) found to express ...unmutated Ig heavy chains (IgH) encoded by a 51p1 allele of IGHV1-69 among 1846 CLL patients examined. We found each had at least 98% homology to an identified germline IGKV or IGLV gene. Within the 258 IgH, we identified heavy chain CDR3 (HCDR3) motifs encoded by certain unmutated IGHD and IGHJ genes with restricted reading frames. Frequent and restricted use of particular IGKV and IGLV genes revealed nonstochastic pairing of disparate Ig light chains (IgL) with IgH that had restricted HCDR3 motifs designated CLL69A, -B, -C, and -D. Eighty-six percent (19/22) of CLL cases that expressed motif CLL69B encoded by IGHD2-2/IGHJ6 had distinctive IgL encoded by IGKV1-39. Similarly, 83% (5/6) of samples with motif CLL69D encoded by IGHD2-2/IGHJ6 expressed IGKV3-11, 100% (25/25) with motif CLL69A encoded by IGHD3-16/IGHJ3 used IGKV3-20, and 77% (10/13) with motif CLL69C encoded by IGHD3-3/IGHJ6 expressed IGLV3-9. This study reveals nonstochastic pairing of IgH with particular IgL that is predicated upon Ig HCDR3 structure, providing compelling evidence for selection of antibodies expressed in CLL by conventional antigens.
Random mutagenesis and phenotype screening provide a powerful method for dissecting microbial functions, but their results can be laborious to analyze experimentally. Each mutant strain may contain ...50-100 random mutations, necessitating extensive functional experiments to determine which one causes the selected phenotype. To solve this problem, we propose a "Phenotype Sequencing" approach in which genes causing the phenotype can be identified directly from sequencing of multiple independent mutants. We developed a new computational analysis method showing that 1. causal genes can be identified with high probability from even a modest number of mutant genomes; 2. costs can be cut many-fold compared with a conventional genome sequencing approach via an optimized strategy of library-pooling (multiple strains per library) and tag-pooling (multiple tagged libraries per sequencing lane). We have performed extensive validation experiments on a set of E. coli mutants with increased isobutanol biofuel tolerance. We generated a range of sequencing experiments varying from 3 to 32 mutant strains, with pooling on 1 to 3 sequencing lanes. Our statistical analysis of these data (4099 mutations from 32 mutant genomes) successfully identified 3 genes (acrB, marC, acrA) that have been independently validated as causing this experimental phenotype. It must be emphasized that our approach reduces mutant sequencing costs enormously. Whereas a conventional genome sequencing experiment would have cost $7,200 in reagents alone, our Phenotype Sequencing design yielded the same information value for only $1200. In fact, our smallest experiments reliably identified acrB and marC at a cost of only $110-$340.
•Participants who undergo gene therapy for ADA-SCID may harbor underlying germline alterations that increase risk of malignancy.•Participants who undergo gene therapy for ADA-SCID may have decreased ...telomere length after busulfan conditioning.
Autologous stem cell transplant with gene therapy (ASCT-GT) provides curative therapy while reducing pretransplant immune-suppressive conditioning and eliminating posttransplant immune suppression. Clonal hematopoiesis of indeterminate potential (CHIP)–associated mutations increase and telomere lengths (TLs) shorten with natural aging and DNA damaging processes. It is possible that, if CHIP is present before ASCT-GT or mutagenesis occurs after busulfan exposure, the hematopoietic stem cells carrying these somatic variants may survive the conditioning chemotherapy and have a selective reconstitution advantage, increasing the risk of hematologic malignancy and overall mortality. Seventy-four peripheral blood samples (ranging from baseline to 120 months after ASCT-GT) from 10 pediatric participants who underwent ASCT-GT for adenosine deaminase–deficient severe combined immune deficiency (ADA-SCID) after reduced-intensity conditioning with busulfan and 16 healthy controls were analyzed for TL and CHIP. One participant had a significant decrease in TL. There were no CHIP-associated mutations identified by the next-generation sequencing in any of the ADA-SCID participants. This suggests that further studies are needed to determine the utility of germline analyses in revealing the underlying genetic risk of malignancy in participants who undergo gene therapy. Although these results are promising, larger scale studies are needed to corroborate the effect of ASCT-GT on TL and CHIP. This trial was registered at www.clinicaltrials.gov as #NCT00794508.
Analysis of the immunoglobulin (Ig) heavy chains expressed by the leukemic B cells of patients with chronic lymphocytic leukemia (CLL) has demonstrated that expression of Ig variable heavy chain (VH) ...genes in CLL is not random. Certain VH genes are more frequently expressed in CLL than in the normal adult B cell repertoire, and some, such as the 51p1 allele of VH1-69, also use of certain diversity (D) and junctional (JH) gene segments that encode third complementarity determining regions (CDR3) with conserved molecular structures. We identified 15 CLL cases among 1,220 examined that express nearly identical Ig heavy and light chains, encoded by 51p1/D3-16/JH3 and VKA27, respectively (Blood , 104:2499, 2004). The highly restricted and virtually identical structure of these B cell receptors strongly suggests selection for Ig in CLL that have a particular binding activity. However, little information is currently available about the light chains expressed by CLL B cells that have 51p1-encoded Ig heavy chains that use other D and JH segments encoding CDR3 that also are repeatedly observed in this disease. We analyzed the VL genes used by 235 CLL cases found to express 51p1-encoded Ig heavy chains among 1,605 CLL patients examined. First, we find restricted light chain isotype expression, as 72% of samples express kappa and 28% express lambda light chains, compared to 65% kappa and 35% lambda within the cohort of all 1,605 CRC CLL samples, and about 60% kappa and 40% lambda expression in normal blood B cells. Nucleotide sequence analysis of the Ig light chain V gene used by these 235 cases revealed that each had greater than 98% homology to an identified germline VK or Vl gene. Additionally, we identified non-stochastic pairing of particular VK and Vl genes with 51p1-encoded heavy chains that have highly-conserved CDR3. Twenty of the 235 cases (8.5%) were found to have Ig light chains encoded by VKO2. Seventeen (85%) of such cases had 51p1-encoded Ig heavy chains that used D2-2 and JH6, 15 of which had nearly identical CDR3 using the amino acid motif DIVVVPAAI. The VKO2-encoded light chains paired with these Ig heavy chains all had nearly identical CDR3 with the amino acid sequence motif QQSYSTPRT. Similarly, seven of the 235 cases (3%) were found to have Ig light chains encoded by Vl3-9. Six (86%) of such cases had 51p1-encoded Ig heavy chains that used D3-3 and JH6, and all had highly conserved heavy chain CDR3 with the amino acid motif YDFWSGYYPNYYYYGMDV. The Vl3-9-encoded light chains paired with these Ig heavy chains all had nearly identical CDR3 with the amino acid sequence motif QVWDSSTXV. Finally, we identified seven additional samples that express a heavy chain using D3-16 and JH3 that have nearly identical CDR3 amino acid sequences GGGYDYIWGSYRPNDAFDI, and also express light chains encoded by VKA27. These seven samples combined with the previous 15 represent all of the 51p1-encoded heavy chains that utilize D3-16 and JH3, as well as 52% (22 of 42) of all 51p1-encoded CLL samples that express VKA27-encoded light chains. These studies reveal for the first time that CLL cases using the same unmutated Ig heavy chain have non-stochastic pairing with disparate Ig light chains that is predicated upon the Ig heavy chain CDR3 structure. Because the CDR3 typically forms a major part of antibody binding site(s) for antigen, these data provide compelling evidence for antigen selection of the antibodies expressed in CLL.
Patients with chronic lymphocytic leukemia (CLL) cells that express unmutated immunoglobulin (Ig) heavy chain variable region genes (IgVH genes) generally have a more aggressive clinical course than ...do patients with leukemia cells that express mutated IgVH. The reason(s) accounting for this are not known. Microarray gene expression analyses revealed that CLL cells that express unmutated IgVH could be distinguished from the leukemia cells that express mutated IgVH via the differential expression of a relatively small number of genes, one of which encodes the zeta-associated chain of 70kD (ZAP-70), which generally is expressed by CLL cells that express unmutated IgVH. Although the expression of ZAP-70 is associated with expression of unmutated IgVH in CLL, this association is not absolute. This was the case for a pair of monozygotic twins who both developed CLL at age 57. Although each of the twins had leukemia cells that expressed mutated IgVH, only one of the twins had leukemia cells that lacked expression of ZAP-70 protein and has indolent, non-progressive disease (Blood 100: 4609–14, 2002). We performed microarray analysis using Affymetrix HG-U133A array on the isolated leukemia cells of each twin to define the genes that were differentially expressed between the two. In addition to ZAP-70, we found that the CLL cells of the twin with progressive disease also expressed the inducible co-stimulatory molecule (ICOS), a member of the CD28/CTLA-4 family of immune accessory co-stimulatory molecules that ordinarily only is expressed by activated T cells. Expression of ICOS protein by this leukemia B cell population, but not by the CLL B cells population of the other twin, was confirmed using fluorochrome-labeled anti-ICOS mAb and flow cytometry. We examined the CLL B cells from 58 additional patients for expression of ICOS by flow cytometry and found that 16 (28%) also expressed ICOS. We found that expression of ICOS was associated with expression of ZAP-70, as assessed via flow cytometry and immunoblot analyses. Whereas 14 of the 29 ZAP-70+ cases expressed ICOS, only 2 of the 29 ZAP-70-negative cases expressed this immune co-stimulatory molecule. Nevertheless, we found that nearly all of the 56 of the 58 cases expressed B7h, the ligand for ICOS. The two cases that did not express detectable B7h expressed ZAP-70 and were ICOS+. In preliminary studies, we found that treatment of ICOS-negative, ZAP-70+ CLL cells (n = 2) with goat anti-human Ig could induce expression of ICOS, suggesting that, as on T cells, this molecule also might be inducible in some cases of B cell CLL. Culture of ICOS+ CLL cells with an anti-B7h mAb capable of blocking ICOS-B7h interactions significantly enhanced ICOS surface expression, as assess by flow cytometry, suggesting that B7h may down-modulate ICOS through paracrine/autocrine receptor-ligand interactions. Because of this we evaluated for functional expression of ICOS on CLL B cells. We found that ligation of ICOS could induce enhanced signaling via the PI3K/Akt pathway in isolated CLL B cells, resulting in enhanced phosphorylation and activation of Akt. As such, we speculate that the expression of ICOS and its ligand in B cell CLL may enhance leukemia cell survival and/or proliferation, potentially contributing to the more aggressive disease observed in some patients with this disease.
Several recent studies have pointed towards a number of sets of CLL patients with highly similar IgV genes, both in terms of V, D, J segment and light chain use and also heavy chain third ...complementarity determining region (CDR3) architecture and amino acid composition. These findings support the notion that antigen may drive development or perpetuation of the leukemic cells. To effectively mine the available Ig sequence databases, we developed a novel sequence similarity and clustering algorithm that incorporates the mechanistic knowledge of IgV gene recombination. CDR3 sequences were initially aligned using the conventional blosum62 based scoring matrix, then rescored based on the junctional annotations. In this way, the method gives greater weight to sequence similarity created as a consequence of the VDJ recombination process, rather than simple germline homology. This modified scoring matrix allows the creation of more robust sequence “clusters” and is not restricted to sequences composed of the same germline genes. Preliminary analysis with this method on a collection of more than 1000 CLL IgV gene sequences has identified over 40 clusters, including all that have been previously described. Interestingly, a species abundance estimator indicates additional clusters of IgV genes in CLL remain to be discovered. Additionally, we performed a focused evaluation of over 100 VH4-34 containing sequences expressed by CLL cells of unrelated patients. The VH4-34 gene is among the most commonly used IVH genes expressed in CLL, has a curious bi-phasic distribution of mutational frequencies among different CLL cases, and can encode antibodies with specificity for the linear polylactosamine carbohydrate antigen “i” found on neonatal red blood cells. Prior studies by the Chiorazzi group identified a subgroup of patients with CLL cells that expressed remarkably similar mutated VH4-34 genes encoding isotype-switched Ig. Using the method described above, seven additional clusters of CLL cases that expressed highly related VH4-34-encoded Ig were identified, including three clusters containing sequences with a mutated VH4-34. The mutations seen within these clusters have a spectra that is distinct from other VH4-34 sequences from CLL, normal plasma cells, or marginal zone B cells. Furthermore, within each cluster there were conserved replacement mutations not commonly found in the other VH4-34 sequences. This clearly indicates specific selective pressures subsequent to IgV gene rearrangement and implies that the expressed Ig were selected for binding to several distinct antigens or epitopes. However, redundant antigen specificities encoded by different sequence clusters can not be excluded and the number of driving antigens may still be quite restricted. Comparative analysis of normal sequence collections is ongoing.
PDF
